@article {pmid39880121,
year = {2025},
author = {Almeida-Santos, AC and Novais, C and Peixe, L and Freitas, AR},
title = {Vancomycin-Resistant Enterococcus faecium: A current perspective on resilience, adaptation, and the urgent need for novel strategies.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.01.016},
pmid = {39880121},
issn = {2213-7173},
abstract = {Vancomycin-resistant Enterococcus faecium (VREfm) has become a critical opportunistic pathogen, urgently requiring new antimicrobial strategies due to its rising prevalence and significant impact on patient safety and healthcare costs. VREfm continues to evolve through mutations and the acquisition of new genes via horizontal gene transfer, contributing to resistance against several last-resort antibiotics. Although primarily hospital-associated, VREfm is also detected in the community, food chain, livestock, and environmental sources like wastewater, indicating diverse transmission pathways and the need for a One Health approach. Advances in genomics have shed light on VREfm's persistence in hospital settings, particularly its adaptation to the gastrointestinal tract of hospitalized patients, recent clonal shifts, and the dominance of specific clonal lineages. Despite extensive research, significant gaps remain in understanding the molecular mechanisms behind VREfm's unique adaptation to clinical environments. In this review, we aim to present an overview of VREfm current prevalence, mechanisms of resistance, and unveil the adaptive traits that have facilitated VREfm's rise and global success. A particular focus is given to key plasmids, namely linear plasmids, virulence factors, and bacteriocins as potential drivers in the global emergence of the ST78 clonal lineage. We also address diagnostic challenges and the limited treatment options available for VREfm, as well as emerging antibiotic alternatives aimed at restoring gut microbiota balance and curbing VREfm proliferation. A multifaceted approach combining research, clinical practices, and public health policies is crucial to mitigate the impact of this superbug and preserve antimicrobial effectiveness for future generations.},
}

@article {pmid39878503,
year = {2025},
author = {Ndovie, W and Havránek, J and Leconte, J and Koszucki, J and Chindelevitch, L and Adriaenssens, EM and Mostowy, RJ},
title = {Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0166124},
doi = {10.1128/msystems.01661-24},
pmid = {39878503},
issn = {2379-5077},
abstract = {Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference data sets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline optimized for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%. Using a rigorous simulation framework, we demonstrate MANIAC's accuracy and scalability compared to existing approaches, even to data sets of hundreds of thousands of viral genomes. Applying MANIAC to a curated data set of complete bacterial dsDNA viruses revealed a multimodal ANI distribution, with a distinct gap around 80%, akin to the bacterial ANI gap (~90%) but shifted, likely due to viral-specific evolutionary processes such as recombination dynamics and mosaicism. We then evaluated ANI and AF as predictors of genus-level taxonomy using a logistic regression model. We found that this model has strong predictive power (PR-AUC = 0.981), but that it works much better for virulent (PR-AUC = 0.997) than temperate (PR-AUC = 0.847) bacterial viruses. This highlights the complexity of taxonomic classification in temperate phages, known for their extensive mosaicism, and cautions against over-reliance on ANI in such cases. MANIAC can be accessed at https://github.com/bioinf-mcb/MANIAC.IMPORTANCEWe introduce a novel computational pipeline called MANIAC, designed to accurately assess average nucleotide identity (ANI) and alignment fraction (AF) between diverse viral genomes, scalable to data sets of over 100k genomes. Using computer simulations and real data analyses, we show that MANIAC could accurately estimate genetic relatedness between pairs of viral genomes of around 60%-70% ANI. We applied MANIAC to investigate the question of ANI discontinuity in bacterial dsDNA viruses, finding evidence for an ANI gap, akin to the one seen in bacteria but around ANI of 80%. We then assessed the ability of ANI and AF to predict taxonomic genus boundaries, finding its strong predictive power in virulent, but not in temperate phages. Our results suggest that bacterial dsDNA viruses may exhibit an ANI threshold (on average around 80%) above which recombination helps maintain population cohesiveness, as previously argued in bacteria.},
}

@article {pmid39874786,
year = {2025},
author = {Chen, Y and Liu, Y and Zhao, C and Ma, J and Guo, J},
title = {Antibiotic resistance gene pollution in poultry farming environments and approaches for mitigation: A system review.},
journal = {Poultry science},
volume = {104},
number = {3},
pages = {104858},
doi = {10.1016/j.psj.2025.104858},
pmid = {39874786},
issn = {1525-3171},
abstract = {Antibiotic resistance genes (ARG) pollution in poultry farming environments has become increasingly critical, primarily driven by the widespread use of antibiotics in animal husbandry. Prolonged antibiotic use has led to the emergence of ARGs and antibiotic-resistant bacteria, spreading via horizontal and vertical gene transfer. The complexity of ARG pollution in poultry farming arises from the unique farming practices, physiological characteristics of poultry, and manure management methods, with manure, wastewater, and air serving as significant vectors for ARG dissemination. Current research indicates that the spread of ARGs poses a significant threat to ecosystems and public health. In response to this growing concern, this review outlines the sources, distribution characteristics, and transmission mechanisms of ARGs in poultry farming environments. It also evaluates the efficacy of existing waste treatment technologies in mitigating ARG contamination. The review proposes several strategies to control ARG dissemination effectively, including reducing antibiotic usage, improving farming practices, optimizing waste management, and strengthening regulatory oversight. It also highlights the need for further research to address existing knowledge gaps and explore more efficient pollution control technologies and management measures. This review aims to provide theoretical support for protecting the environment and public health in the context of poultry farming.},
}

@article {pmid39874387,
year = {2025},
author = {Li, Y and Pulford, CV and Díaz, P and Perez-Sepulveda, BM and Duarte, C and Predeus, AV and Wiesner, M and Heavens, D and Low, R and Schudoma, C and Montaño, A and Hall, N and Moreno, J and Hinton, JCD},
title = {Potential links between human bloodstream infection by Salmonella enterica serovar Typhimurium and international transmission to Colombia.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {1},
pages = {e0012801},
doi = {10.1371/journal.pntd.0012801},
pmid = {39874387},
issn = {1935-2735},
abstract = {Salmonella enterica serovar Typhimurium is a prevalent food-borne pathogen that is usually associated with gastroenteritis infection. S. Typhimurium is also a major cause of bloodstream infections in sub-Saharan Africa, and is responsible for invasive non-typhoidal Salmonella (iNTS) disease. The pathogen also causes bloodstream infection in Colombia, but there has been a lack of information about the S. Typhimurium isolates that were responsible. Here, we investigated the genomic characteristics of 270 S. Typhimurium isolates from bloodstream infection patients in Colombia, collected between 1997 and 2017. We used whole-genome sequencing to analyse multidrug-resistant (MDR) profiles, plasmid distribution, and to define phylogenetic relationships. The study identified the distinct sequence types and phylogenetic clusters of S. Typhimurium prevalent in Colombia. The majority of isolates (90.8%) were ST19, which is distinct from the iNTS-associated S. Typhimurium in sub-Saharan Africa (ST313). The two prominent clusters of MDR S. Typhimurium were either DT104 or closely related to the LT2 reference strain. We used a phylogenetic approach to associate the Colombian clusters with global S. Typhimurium isolates from public databases. By putting the Colombian S. Typhimurium isolates in the context of the global spread of DT104, ST313 and LT2-related variants, we found that the Colombian clusters were introduced to the country via multiple independent events that were consistent with international transmission. We suggest that the acquisition of quinolone and chloramphenicol resistance by the Colombian S. Typhimurium isolates was driven by horizontal gene transfer. Three ST313 isolates that caused bloodstream infection in Colombia were identified. These ST313 isolates were related to the Malawian ST313 lineage 3 & UK ST313, and shared a similarly high invasiveness index. To our knowledge, this is the first report of ST313 in Colombia.},
}

@article {pmid38045412,
year = {2025},
author = {Lind, AL and McDonald, NA and Gerrick, ER and Bhatt, AS and Pollard, KS},
title = {Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.20.567959},
pmid = {38045412},
issn = {2692-8205},
support = {K22 AI173181/AI/NIAID NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; R01 HL160862/HL/NHLBI NIH HHS/United States ; },
abstract = {Blastocystis , an obligate host-associated protist, is the most common microbial eukaryote in the human gut and is widely distributed across vertebrate hosts. The evolutionary transition of Blastocystis from its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses revealed significant variation in gene content and genome structure across Blastocystis. Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly larger genomes with longer introns and intergenic regions, and retain canonical stop codons absent in the human-associated strains. Despite these genetic differences, all eight isolates exhibit gene losses linked to the reduced cellular complexity of Blastocystis, including losses of cilia and flagella genes, microtubule motor genes, and signal transduction genes. Isolates from herbivorous tortoises contained higher numbers of plant carbohydrate-metabolizing enzymes, suggesting that like gut bacteria, these protists ferment plant material in the host gut. We find evidence that some of these carbohydrate-metabolizing enzymes were horizontally acquired from bacteria, indicating that horizontal gene transfer is an ongoing process in Blastocystis that has contributed to host-related adaptation. Together, these results highlight substantial genetic and metabolic diversity within the Blastocystis genus, indicating different lineages of Blastocystis have varied ecological roles in the host gut.},
}

@article {pmid39873499,
year = {2025},
author = {Liu, CC and Hsiao, WWL},
title = {Machine learning reveals the dynamic importance of accessory sequences for Salmonella outbreak clustering.},
journal = {mBio},
volume = {},
number = {},
pages = {e0265024},
doi = {10.1128/mbio.02650-24},
pmid = {39873499},
issn = {2150-7511},
abstract = {UNLABELLED: Bacterial typing at whole-genome scales is now feasible owing to decreasing costs in high-throughput sequencing and the recent advances in computation. The unprecedented resolution of whole-genome typing is achieved by genotyping the variable segments of bacterial genomes that can fluctuate significantly in gene content. However, due to the transient and hypervariable nature of many accessory elements, the value of the added resolution in outbreak investigations remains disputed. To assess the analytical value of bacterial accessory genomes in clustering epidemiologically related cases, we trained classifiers on a set of genomes collected from 24 Salmonella enterica outbreaks of food, animal, or environmental origin. The models demonstrated high precision and recall on unseen test data with near-perfect accuracy in classifying clonal and short-term outbreaks. Annotating the genomic features important for cluster classification revealed functional enrichment of molecular fingerprints in genes involved in membrane transportation, trafficking, and carbohydrate metabolism. Importantly, we discovered polymorphisms in mobile genetic elements (MGEs) and gain/loss of MGEs to be informative in defining outbreak clusters. To quantify the ability of MGE variations to cluster outbreak clones, we devised a reference-free tree-building algorithm inspired by colored de Bruijn graphs, which enabled topological comparisons between MGE and standard typing methods. Systematic evaluation of clustering MGEs on an unseen dataset of 34 Salmonella outbreaks yielded mixed results that exemplified the power of accessory sequence variations when core genomes of unrelated cases are insufficiently discriminatory, as well as the distortion of outbreak signals by microevolution events or the incomplete assembly of MGEs.

IMPORTANCE: Gene-by-gene typing is widely used to detect clusters of foodborne illnesses that share a common origin. It remains actively debated whether the inclusion of accessory sequences in bacterial typing schema is informative or deleterious for cluster definitions in outbreak investigations due to the potential confounding effects of horizontal gene transfer. By training machine learning models on a curated set of historical Salmonella outbreaks, we revealed an enriched presence of outbreak distinguishing features in a wide range of mobile genetic elements. Systematic comparison of the efficacy of clustering different accessory elements against standard sequence typing methods led to our cataloging of scenarios where accessory sequence variations were beneficial and uninformative to resolving outbreak clusters. The presented work underscores the complexity of the molecular trends in enteric outbreaks and seeks to inspire novel computational ways to exploit whole-genome sequencing data in enteric disease surveillance and management.},
}

@article {pmid39871141,
year = {2025},
author = {Nichio, BTL and Chaves, RBR and Pedrosa, FO and Raittz, RT},
title = {Exploring diazotrophic diversity: unveiling Nif core distribution and evolutionary patterns in nitrogen-fixing organisms.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {81},
pmid = {39871141},
issn = {1471-2164},
mesh = {*Nitrogen Fixation/genetics ; *Phylogeny ; *Evolution, Molecular ; *Nitrogenase/metabolism/genetics ; Bacterial Proteins/genetics/metabolism ; Gene Duplication ; Gene Transfer, Horizontal ; },
abstract = {BACKGROUND: Diazotrophs carry out biological nitrogen fixation (BNF) using the nitrogenase enzyme complex (NEC), which relies on nitrogenase encoded by nif genes. Horizontal gene transfer (HGT) and gene duplications have created significant diversity among these genes, making it challenging to identify potential diazotrophs. Previous studies have established a minimal set of Nif proteins, known as the Nif core, which includes NifH, NifD, NifK, NifE, NifN, and NifB. This study aimed to identify potential diazotroph groups based on the Nif core and to analyze the inheritance patterns of accessory Nif proteins related to Mo-nitrogenase, along with their impact on N2 fixation maintenance.

RESULTS: In a systematic study, 118 diazotrophs were identified, resulting in a database of 2,156 Nif protein sequences obtained with RAFTS³G. Using this Nif database and a data mining strategy, we extended our analysis to 711 species and found that 544 contain the Nif core. A partial Nif core set was observed in eight species in this study. Finally, we cataloged 662 species with Nif core, of which 52 were novel. Our analysis generated 10,076 Nif proteins from these species and revealed some Nif core duplications. Additionally, we determined the optimal cluster value (k = 10) for analyzing diazotrophic diversity. Combining synteny and phylogenetic analyses revealed distinct syntenies in the nif gene composition across ten groups.

CONCLUSIONS: This study advances our understanding of the distribution of nif genes, aiding in the prediction and classification of N₂-fixing organisms. Furthermore, we present a comprehensive overview of the diversity, distribution, and evolutionary relationships among diazotrophic organisms associated with the Nif core. The analysis revealed the phylogenetic and functional organization of different groups, identifying synteny patterns and new nif gene arrangements across various bacterial and archaeal species.The identified groups serve as a valuable framework for further exploration of the molecular mechanisms underlying biological nitrogen fixation and its evolutionary significance across different bacterial lineages.},
}

*Nitrogen Fixation/genetics
*Phylogeny
*Evolution, Molecular
*Nitrogenase/metabolism/genetics
Bacterial Proteins/genetics/metabolism
Gene Duplication
Gene Transfer, Horizontal

@article {pmid39870251,
year = {2025},
author = {Oubohssaine, M and Rabeh, K and Hnini, M},
title = {Symbiosis vs Pathogenesis in Plants: Reflections and Perspectives.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107333},
doi = {10.1016/j.micpath.2025.107333},
pmid = {39870251},
issn = {1096-1208},
abstract = {Plant-microbe partnerships constitute a complex and intricately woven network of connections that have evolved over countless centuries, involving both cooperation and antagonism. In various contexts, plants and microorganisms engage in mutually beneficial partnerships that enhance crop health and maintain balance in ecosystems. However, these associations also render plants susceptible to a range of pathogens. Understanding the fundamental molecular mechanisms governing these associations is crucial, given the notable susceptibility of plants to external environmental influences. Based on quorum sensing signals, phytohormone, and volatile organic carbon (VOC) production and others molecules, microorganisms influence plant growth, health, and defense responses. This review explores the multifaceted relationships between plants and their associated microorganisms, encompassing mutualism, commensalism, and antagonism. The molecular mechanisms of symbiotic and pathogenic interactions share similarities but lead to different outcomes. While symbiosis benefits both parties, pathogenesis harms the host. Genetic adaptations optimize these interactions, involving coevolution driving process. Environmental factors influence outcomes, emphasizing the need for understanding and manipulation of microbial communities for beneficial results. Research directions include employing multi-omics techniques, functional studies, investigating environmental factors, understanding evolutionary trajectories, and harnessing knowledge to engineer synthetic microbial consortia for sustainable agriculture and disease management.},
}

@article {pmid39812022,
year = {2025},
author = {Gamblin, J and Lambert, A and Blanquart, F},
title = {Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.},
journal = {Molecular biology and evolution},
volume = {42},
number = {1},
pages = {},
doi = {10.1093/molbev/msaf001},
pmid = {39812022},
issn = {1537-1719},
support = {FDT202304016561//Fondation pour la Recherche Médicale/ ; },
mesh = {*Evolution, Molecular ; *Genome, Bacterial ; *Models, Genetic ; *Phylogeny ; *Salmonella enterica/genetics ; Algorithms ; Genes, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {The pangenome of a species is the set of all genes carried by at least one member of the species. In bacteria, pangenomes can be much larger than the set of genes carried by a single organism. Many questions remain unanswered regarding the evolutionary forces shaping the patterns of the presence/absence of genes in pangenomes of a given species. We introduce a new model for bacterial pangenome evolution along a species phylogeny that explicitly describes the timing of appearance of each gene in the species and accounts for three generic types of gene evolutionary dynamics: persistent genes that are present in the ancestral genome, private genes that are specific to a given clade, and mobile genes that are imported once into the gene pool and then undergo frequent horizontal gene transfers. We call this model the Persistent-Private-Mobile (PPM) model. We develop an algorithm fitting the PPM model and apply it to a dataset of 902 Salmonella enterica genomes. We show that the best fitting model is able to reproduce the global pattern of some multivariate statistics like the gene frequency spectrum and the parsimony vs. frequency plot. Moreover, the gene classification induced by the PPM model allows us to study the position of accessory genes on the chromosome depending on their category, as well as the gene functions that are most present in each category. This work paves the way for a mechanistic understanding of pangenome evolution, and the PPM model developed here could be used for dynamics-aware gene classification.},
}

*Evolution, Molecular
*Genome, Bacterial
*Models, Genetic
*Phylogeny
*Salmonella enterica/genetics
Algorithms
Genes, Bacterial
Gene Transfer, Horizontal

@article {pmid39867821,
year = {2025},
author = {Yan, Z and Wang, H and Zhu, Y and Wang, X and Wu, Y and Wang, Y and Zhang, R},
title = {Molecular Epidemiology of Type F Clostridium perfringens Among Diarrheal Patients and Virulence-Resistance Dynamics - 11 Provinces, China, 2024.},
journal = {China CDC weekly},
volume = {7},
number = {3},
pages = {69-76},
pmid = {39867821},
issn = {2096-7071},
abstract = {INTRODUCTION: Type F Clostridium perfringens (C. perfringens) represents a significant pathogen in human gastrointestinal diseases, primarily through its cpe gene encoding C. perfringens enterotoxin (CPE). This investigation examined the prevalence, antimicrobial resistance patterns, and genetic characteristics of Type F C. perfringens within the Chinese population.

METHODS: The study analyzed 2,068 stool samples collected from 11 provincial hospitals in 2024. Antimicrobial susceptibility testing was conducted following Clinical & Laboratory Standards Institute (CLSI) guidelines, while whole-genome sequencing provided detailed genetic profiles. Evolutionary relationships and clonal transmission patterns were investigated through phylogenetic and genetic environment analyses.

RESULTS: The prevalence of Type F C. perfringens was 2.38%, with isolates predominantly identified in human clinical samples and higher detection rates in gastroenterology departments. Notably, 47.1% of isolates demonstrated high resistance to metronidazole, while all exhibited intermediate resistance to erythromycin. Phylogenetic analysis revealed high similarity among isolates from patients within the same province (single-nucleotide polymorphism (SNPs)<100), and genetic environment analysis indicated potential horizontal gene transfer between animal and human strains.

CONCLUSIONS: This investigation predominantly identified Type F C. perfringens in human clinical cases, with sporadic detection in pets and food products. These findings highlight the emergence of Type F C. perfringens outbreaks among diarrheal patients, emphasizing the necessity for targeted interventions as virulence factors increase.},
}

@article {pmid39865504,
year = {2025},
author = {Sharp, PM and Bibollet-Ruche, F and Hahn, BH},
title = {Plasmodium falciparum CyRPA glycan binding does not explain adaptation to humans.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf016},
pmid = {39865504},
issn = {1759-6653},
abstract = {The human malaria parasite Plasmodium falciparum evolved from a parasite that infects gorillas, termed Plasmodium praefalciparum. The sialic acids on glycans on the surface of erythrocytes differ between humans and other apes. It has recently been shown that the P. falciparum cysteine-rich protective antigen (PfCyRPA) binds human sialoglycans as an essential step in the erythrocyte invasion pathway, while that of the chimpanzee parasite Plasmodium reichenowi has affinities matching ape glycans. Two amino acid changes, at sites 154 and 209, were shown to be sufficient to switch glycan binding preferences and inferred to reflect adaptation of P. falciparum to humans. However, we show that sites 154 and 209 are identical in P. falciparum and P. praefalciparum, with no other differences located in or near the CyRPA glycan binding sites. Thus, the gorilla precursor appears to have already been preadapted to bind human sialoglycans.},
}

@article {pmid39862584,
year = {2025},
author = {Zheng, Z and Ji, W and Wang, X and Wang, X and Dai, S and Zhang, Z and Zhang, Y and Wang, X and Cao, S and Chen, M and Xie, B and Feng, J and Wu, D},
title = {Household waste-specific ambient air shows greater inhalable antimicrobial resistance risks in densely populated communities.},
journal = {Waste management (New York, N.Y.)},
volume = {194},
number = {},
pages = {309-317},
doi = {10.1016/j.wasman.2025.01.030},
pmid = {39862584},
issn = {1879-2456},
abstract = {Household waste is a hotspot of antibiotic resistance, which can be readily emitted to the ambient airborne inhalable particulate matters (PM10) during the day-long storage in communities. Nevertheless, whether these waste-specific inhalable antibiotic resistance genes (ARGs) are associated with pathogenic bacteria or pose hazards to local residents have yet to be explored. By high-throughput metagenomic sequencing and culture-based antibiotic resistance validation, we analyzed 108 airborne PM10 and nearby environmental samples collected across different types of residential communities in Shanghai, the most populous city in China. Compared to the cold-dry period, the warm-humid season had significantly larger PM10-associated antibiotic resistomes in all types of residential communities (T-test, P < 0.001), most of airborne ARGs in which were estimatedly originated from disposed household waste (∼ 30 %). In addition, the airborne bacteria were assembled in a deterministic approach (iCAMP, P < 0.01), where the waste-specific bacteria taxa including Acinetobacter, Pseudomonas, Rhodococcus, and Kocuria had the predominant niches in the airborne microbial assemblages. Notably, these waste-sourced bacteria were also identified as the primary airborne hosts of ARGs encoding the aminoglycoside resistances. Among them, some antibiotic resistant human pathogens, such as Pseudomonas aeruginosa and Acinetobacter baumannii, not only exhibited higher ARG horizontal gene transfer (HGT) potential across the microbial assemblages, but also imposed direct infection risks on the local residents by 2 min inhalation exposure per day. When the daily exposure duration increased to 11 min, the infection-induced illness burden became unignorably high, especially in densely populated urban communities, being twofold greater than rural areas.},
}

@article {pmid39862048,
year = {2025},
author = {Colinet, D and Haon, M and Drula, E and Boyer, M and Grisel, S and Belliardo, C and Koutsovoulos, GD and Berrin, JG and Danchin, EG},
title = {Functional carbohydrate-active enzymes acquired by horizontal gene transfer from plants in the whitefly Bemisia tabaci.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf012},
pmid = {39862048},
issn = {1759-6653},
abstract = {Carbohydrate-active enzymes (CAZymes) involved in the degradation of plant cell walls and/or the assimilation of plant carbohydrates for energy uptake are widely distributed in microorganisms. In contrast, they are less frequent in animals, although there are exceptions, including examples of CAZymes acquired by horizontal gene transfer (HGT) from bacteria or fungi in several of phytophagous arthropods and plant-parasitic nematodes. Although the whitefly Bemisia tabaci is a major agricultural pest, knowledge of HGT-acquired CAZymes in this phloem-feeding insect of the Hemiptera order (subfamily Aleyrodinae) is still lacking. We performed a comprehensive and accurate detection of HGT candidates in B. tabaci and identified 136 HGT events, 14 of which corresponding to CAZymes. The B. tabaci HGT-acquired CAZymes were not only of bacterial or fungal origin, but some were also acquired from plants. Biochemical analysis revealed that members of the glycoside hydrolase families 17 (GH17) and 152 (GH152) acquired from plants are functional beta-glucanases with different substrate specificities, suggesting distinct roles. These two CAZymes are the first characterized GH17 and GH152 glucanases in an animal. We identified a lower number of HGT events in the related Aleyrodinae Trialeurodes vaporariorum, with only three HGT-acquired CAZymes, including a GH152 glucanase, with phylogenetic analysis suggesting a unique HGT event in the ancestor of the Aleyrodinae. Another GH152 CAZyme, most likely independently acquired from plants, was also identified in two plant cell-feeding insects of the Thysanoptera order, highlighting the importance of plant-acquired CAZymes in the biology of piercing-sucking insects.},
}

@article {pmid39861970,
year = {2025},
author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I},
title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf014},
pmid = {39861970},
issn = {1751-7370},
abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the reorganisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.},
}

@article {pmid39861872,
year = {2025},
author = {Yakubovskij, VI and Morozova, VV and Kozlova, YN and Tikunov, AY and Fedorets, VA and Zhirakovskaya, EV and Babkin, IV and Bardasheva, AV and Tikunova, NV},
title = {Phage vB_KlebPS_265 Active Against Resistant/MDR and Hypermucoid K2 Strains of Klebsiella pneumoniae.},
journal = {Viruses},
volume = {17},
number = {1},
pages = {},
pmid = {39861872},
issn = {1999-4915},
support = {grant No 122110700002-2//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Klebsiella pneumoniae/virology/genetics ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Genome, Viral ; *Phylogeny ; *Klebsiella Infections/microbiology ; Humans ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Host Specificity ; Gene Transfer, Horizontal ; Sputum/microbiology/virology ; },
abstract = {Klebsiella pneumoniae is an important opportunistic pathogen often resistant to antibiotics. Specific phages can be useful in eliminating infection caused by K. pneumoniae. Klebsiella phage vB_KlebPS_265 (KlebP_265) and its host strain were isolated from the sputum of a patient with Klebsiella infection. KlebP_265 was specific mainly to K. pneumoniae-type K2 strains including hypermucoid strains. Most of the hypermucoid KlebP_265-susceptible strains were antibiotic-resistant. This siphophage demonstrated good lytic activity and stability. The KlebP_265 genome was 46,962 bp and contained 88 putative genes; functions were predicted for 37 of them. No genes encoding integrases, toxins, or antibiotic resistance were found in the genome. So, KlebP_265 could potentially be a therapeutic phage. Comparative analysis indicated that KlebP_265 with the most relative Klebsiella phage DP01 formed the putative Dipiunovirus genus. Genome analysis revealed a large monophyletic group of phages related to KlebP_265 and DP01. This group is divided into two monophyletic clusters of phages forming new putative subfamilies Skatevirinae and Roufvirinae. Phylogenetic analysis showed extensive gene exchange between phages from the putative subfamilies. Horizontal transfer even involved conservative genes and led to clear genomic mosaicism, indicating multiple recombination events in the ancestral phages during evolution.},
}

*Klebsiella pneumoniae/virology/genetics
*Bacteriophages/genetics/classification/isolation & purification/physiology
*Genome, Viral
*Phylogeny
*Klebsiella Infections/microbiology
Humans
Drug Resistance, Multiple, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Host Specificity
Gene Transfer, Horizontal
Sputum/microbiology/virology

@article {pmid39809568,
year = {2025},
author = {Simões de Oliveira, G and Lentz, SAM and Müller, CZ and Guerra, RR and Dalmolin, TV and Volpato, FCZ and de Lima-Morales, D and Lamb Wink, P and Barth, AL and Rabinowitz, P and Martins, AF},
title = {Resistome and plasmidome genomic features of mcr-1.1-harboring Escherichia coli: a One Health approach.},
journal = {Journal of applied microbiology},
volume = {136},
number = {1},
pages = {},
doi = {10.1093/jambio/lxaf019},
pmid = {39809568},
issn = {1365-2672},
support = {//INPRA/ ; 465718/2014-0//CNPq/ ; 17/2551-0000514-7//FAPERGS/ ; 2022-0283//FIPE/ ; //HCPA/ ; },
mesh = {*Escherichia coli/genetics/drug effects ; *Plasmids/genetics ; Animals ; *Escherichia coli Proteins/genetics ; Brazil ; *Chickens/microbiology ; *Anti-Bacterial Agents/pharmacology ; Swine ; *Colistin/pharmacology ; Humans ; *Microbial Sensitivity Tests ; *Escherichia coli Infections/microbiology/veterinary ; One Health ; Drug Resistance, Bacterial/genetics ; Whole Genome Sequencing ; Drug Resistance, Multiple, Bacterial/genetics ; Farms ; Gene Transfer, Horizontal ; Genome, Bacterial ; },
abstract = {AIMS: This study evaluated the phenotypic and genotypic traits of mcr-1.1-harboring Escherichia coli isolates from chickens, pigs, humans, and farm environments. The resistome and the mobile genetic elements associated with the spread of mcr-1.1 in Southern Brazil were also characterized.

METHODS AND RESULTS: The 22 mcr-1.1-harboring E. coli isolates from different origins were selected for antimicrobial susceptibility testing and whole genome sequencing for characterization of the resistome, plasmids, and sequence types. All isolates presented several resistance genes and harbored the mcr-1.1 gene in a highly similar IncX4 plasmid. Furthermore, the mcr-1.1 gene co-occurred with the mcr-3.12 gene in a multidrug-resistant isolate from the farm environment.

CONCLUSIONS: These findings demonstrate that the mcr-1.1 gene in E. coli isolates from Brazil is spreading mainly by horizontal transfer of the IncX4 plasmid. The co-occurrence of mcr-1.1 and mcr-3.12 highlights pig farming as an important reservoir of colistin resistance.},
}

*Escherichia coli/genetics/drug effects
*Plasmids/genetics
Animals
*Escherichia coli Proteins/genetics
Brazil
*Chickens/microbiology
*Anti-Bacterial Agents/pharmacology
Swine
*Colistin/pharmacology
Humans
*Microbial Sensitivity Tests
*Escherichia coli Infections/microbiology/veterinary
One Health
Drug Resistance, Bacterial/genetics
Whole Genome Sequencing
Drug Resistance, Multiple, Bacterial/genetics
Farms
Gene Transfer, Horizontal
Genome, Bacterial

@article {pmid39637801,
year = {2025},
author = {Zhang, S and Zheng, S and Gong, Y and Wang, Y and Wei, Q and Zhu, Y and Liu, L and Wu, R and Du, S},
title = {Does the herbicide napropamide exhibit enantioselective effects across genus plasmid transfer from Escherichia coli to Bacillus subtilis?.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136704},
doi = {10.1016/j.jhazmat.2024.136704},
pmid = {39637801},
issn = {1873-3336},
mesh = {*Escherichia coli/drug effects/genetics ; *Bacillus subtilis/drug effects/genetics ; *Herbicides/toxicity/chemistry ; *Plasmids/genetics ; Stereoisomerism ; Molecular Docking Simulation ; Gene Transfer, Horizontal ; Conjugation, Genetic/drug effects ; Reactive Oxygen Species/metabolism ; },
abstract = {The dissemination of plasmid-borne antibiotic resistance genes (ARGs) into the environment is an urgent concern. However, the enantioselective effects of herbicides on plasmid conjugation among bacterial genera and their underlying mechanisms remain unclear. This study demonstrates for the first time that the herbicide napropamide (NAP), commonly used in vegetable fields, exhibits a concentration-dependent effect on the transfer efficiency of the pBE2R plasmid from Escherichia coli to Bacillus subtilis. Notably, at a concentration of 5 mg L[-1], R-NAP increased transfer efficiency by threefold compared to the S-enantiomer. Scanning electron microscopy revealed that R-NAP caused less structural damage to bacteria than S-NAP but more effectively reduced cell wall components (lipopolysaccharides and peptidoglycan) in donor and recipient bacteria, increasing reactive oxygen species levels and membrane permeability. Transcriptomic analysis indicated that NAP enantiomers altered the expression of genes related to membrane transport activity and transposons. Cross-domain network analysis identified yieK, ygeH, and ydbL as key genes mediating conjugation transfer. Molecular docking results showed that NAP likely interacts hydrophobically with the active sites of the proteins encoded by these genes. In conclusion, herbicides like R-NAP should be carefully managed in fields irrigated with livestock manure to mitigate the risk of ARG transfer and accumulation in crops.},
}

*Escherichia coli/drug effects/genetics
*Bacillus subtilis/drug effects/genetics
*Herbicides/toxicity/chemistry
*Plasmids/genetics
Stereoisomerism
Molecular Docking Simulation
Gene Transfer, Horizontal
Conjugation, Genetic/drug effects
Reactive Oxygen Species/metabolism

@article {pmid39859430,
year = {2025},
author = {Yuan, Z and Zhang, J and Duan, D},
title = {Vanadium-Dependent Haloperoxidase Gene Evolution in Brown Algae: Evidence for Horizontal Gene Transfer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
pmid = {39859430},
issn = {1422-0067},
support = {2022HWYQ-087//Shandong Province/ ; 41806202//National Natural Science Foundation of China/ ; 133137KYSB20210034//Chinese Academy of Sciences/ ; },
mesh = {*Gene Transfer, Horizontal ; *Evolution, Molecular ; *Phaeophyceae/genetics ; *Phylogeny ; *Peroxidases/genetics/metabolism ; Vanadium ; },
abstract = {Compared with green plants, brown algae are characterized by their ability to accumulate iodine, contributing to their ecological adaptability in high-iodide coastal environments. Vanadium-dependent haloperoxidase (V-HPO) is the key enzyme for iodine synthesis. Despite its significance, the evolutionary origin of V-HPO genes remains underexplored. This study investigates the genomic and evolutionary dynamics of V-HPOs in brown algae, focusing on Laminariales species, particularly Saccharina japonica. Genomic analyses revealed the extensive expansion of the V-HPO gene family in brown algae, with 88 V-HPOs identified in S. japonica, surpassing the number in red algae. Phylogenetic analysis demonstrated distinct evolutionary divergence between brown and red algal V-HPOs, with the brown algal clade closely related to bacterial V-HPOs. These findings suggest horizontal gene transfer (HGT) played a key role in acquiring V-HPO genes, particularly from Acidobacteriota, a bacterial phylum known for genomic plasticity. Additionally, enriched active transposable elements were identified around V-HPO genomic clusters, highlighting their role in tandem gene duplications and rapid HGT processes. Expression profiling further revealed dynamic regulation of V-HPOs in response to environmental conditions. This study provides new insights into how HGT has driven kelp genomic adaptations and enhances understanding of marine ecological success and evolutionary processes.},
}

*Gene Transfer, Horizontal
*Evolution, Molecular
*Phaeophyceae/genetics
*Phylogeny
*Peroxidases/genetics/metabolism
Vanadium

@article {pmid39859334,
year = {2025},
author = {Wang, C and Zhao, R and Yang, W and Jiang, W and Tang, H and Du, S and Chen, X},
title = {Cell-to-Cell Natural Transformation Mediated Efficient Plasmid Transfer Between Bacillus Species.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
pmid = {39859334},
issn = {1422-0067},
support = {31970030//National Natural Science Foundation of China/ ; J1103513//National Fund for Fostering Talents of Basic Sciences/ ; None//Research (Innovative) Fund of the Laboratory of Wuhan University./ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Transformation, Bacterial ; Bacillus/genetics ; Bacillus subtilis/genetics ; Conjugation, Genetic ; },
abstract = {Horizontal gene transfer (HGT) plays a pivotal role in bacterial evolution, shaping the genetic diversity of bacterial populations. It can occur through mechanisms such as conjugation, transduction, and natural transformation. Bacillus subtilis, a model Gram-positive bacterium, serves not only as a robust system for studying HGT but also as a versatile organism with established industrial applications, such as producing industrial enzymes, antibiotics, and essential metabolites. In this study, we characterize a novel method of plasmid transfer, termed Cell-to-Cell Natural Transformation for Plasmid Transfer (CTCNT-P), which efficiently facilitates plasmid transfer between naturally competent B. subtilis strains. This method involves co-culturing donor and recipient cells under antibiotic stress and achieves significantly higher efficiency compared to traditional methods such as Spizizen medium or electroporation-mediated transformation. Importantly, we demonstrate that CTCNT-P is applicable for plasmid transformation in wild B. subtilis isolates from natural environments and other Bacillus species, including Bacillus amyloliquefaciens, Bacillus licheniformis, and Bacillus thuringiensis. The simplicity and efficiency of CTCNT-P highlight its strong potential for industrial applications, including genetic modification of wild Bacillus strains for synthetic biology and the development of biocontrol agents.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Transformation, Bacterial
Bacillus/genetics
Bacillus subtilis/genetics
Conjugation, Genetic

@article {pmid39859326,
year = {2025},
author = {Kusada, H and Tamaki, H},
title = {Evidence for the Worldwide Distribution of a Bile Salt Hydrolase Gene in Enterococcus faecium Through Horizontal Gene Transfer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
doi = {10.3390/ijms26020612},
pmid = {39859326},
issn = {1422-0067},
support = {JPMJGX23B2//Japan Science and Technology Agency/ ; 21ae0121047h0001//Japan Agency for Medical Research and Development/ ; },
mesh = {*Enterococcus faecium/genetics/enzymology ; *Amidohydrolases/genetics/metabolism ; *Gene Transfer, Horizontal ; *Phylogeny ; Humans ; Bacterial Proteins/genetics/metabolism ; Plasmids/genetics ; Bile Acids and Salts/metabolism ; },
abstract = {Bile salt hydrolase (BSH), a probiotic-related enzyme with cholesterol-assimilating and anti-hypercholesterolemic abilities, has been isolated from intestinal bacteria; however, BSH activity of bacteria in bile-salt-free (non-intestinal) environments is largely unknown. Here, we aimed to identify BSH from non-intestinal Enterococcus faecium and characterize its enzymatic function. We successfully isolated a plasmid-encoded bsh (efpBSH) from E. faecium, and the recombinant EfpBSH showed BSH activity that preferentially hydrolyzed taurine-conjugated bile salts, unlike the activity of known BSHs. EfpBSH functioned optimally at pH 4.0 and 50 °C. EfpBSH exhibited very low amino acid sequence similarity (48.46%) to EfBSH from E. faecalis T2 isolated from human urine, although 241 sequences with 100% identity to EfpBSH were found in both plasmids and chromosomes of E. faecium strains inhabiting intestinal and non-intestinal environments. Phylogenetically, EfpBSH was not affiliated with any known BSH phylogroup and was clearly distinguished from previously identified BSHs from intestinal lactic acid bacteria. Our genome database analysis demonstrated that horizontal gene transfer causes global efpBSH distribution among E. faecium strains in various environments (soil, water, and intestinal samples) and geographical regions (Asia, Africa, Europe, North America, South America, and Australia/Oceania). Overall, our findings are the first to indicate that BSH is not an intestine-specific enzyme and that hitherto-overlooked probiotic candidates with BSH activity can exist in diverse environments.},
}

*Enterococcus faecium/genetics/enzymology
*Amidohydrolases/genetics/metabolism
*Gene Transfer, Horizontal
*Phylogeny
Humans
Bacterial Proteins/genetics/metabolism
Plasmids/genetics
Bile Acids and Salts/metabolism

@article {pmid39859280,
year = {2025},
author = {Liu, X and Luo, H and Liu, ZJ and Yang, BY},
title = {Mitochondrial Genome Characteristics Reveal Evolution of Danxiaorchis yangii and Phylogenetic Relationships.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
doi = {10.3390/ijms26020562},
pmid = {39859280},
issn = {1422-0067},
mesh = {*Phylogeny ; *Genome, Mitochondrial ; *Orchidaceae/genetics/classification ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Base Composition ; RNA, Transfer/genetics ; Codon Usage ; },
abstract = {Danxiaorchis yangii is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus Danxiaorchis in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding genes (PCGs), 16 tRNAs, and 2 rRNAs, and conducted analyses of relative synonymous codon usage (RSCU), repeat sequences, horizontal gene transfers (HGTs), and gene selective pressure (dN/dS). Additionally, we sequenced and assembled its plastome, which has a reduced size of 110,364 bp (GC content: 36.60%), comprising 48 PCGs, 26 tRNAs, and 4 rRNAs. We identified 64 potential chloroplast DNA fragments transferred to the mitogenome. Phylogenomic analysis focusing on 33 mitogenomes, with Vitis vinifera as the outgroup, indicated that D. yangii is grouped as follows: D. yangii + ((Dendrobium wilsonii + Dendrobium wilsonii henanense) + Phalaenopsis aphrodite). Phylogenetic analysis based on 83 plastid PCGs from these species showed that D. yangii is grouped as follows: (D. yangii + Pha. aphrodite) + (Den. wilsonii + Den. henanense). Gene selective pressure analysis revealed that most mitochondrial and plastid genes in D. yangii are under purifying selection, ensuring functional stability, and certain genes may have undergone positive selection or adaptive evolution, reflecting the species' adaptation to specific ecological environments. Our study provides valuable data on the plastomes and mitogenomes of D. yangii and lays the groundwork for future research on genetic variation, evolutionary relationships, and the breeding of orchids.},
}

*Phylogeny
*Genome, Mitochondrial
*Orchidaceae/genetics/classification
*Evolution, Molecular
Gene Transfer, Horizontal
Base Composition
RNA, Transfer/genetics
Codon Usage

@article {pmid39858976,
year = {2025},
author = {He, Y and Dykes, GE and Kanrar, S and Liu, Y and Gunther, NW and Counihan, KL and Lee, J and Capobianco, JA},
title = {Comparative Genomic Analysis of Campylobacter Plasmids Identified in Food Isolates.},
journal = {Microorganisms},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/microorganisms13010206},
pmid = {39858976},
issn = {2076-2607},
support = {Current Research Information System number 8072-42000-093//U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), National Program 108/ ; },
abstract = {Campylobacter is one of the leading bacterial causes of gastroenteritis worldwide. It frequently contaminates poultry and other raw meat products, which are the primary sources of Campylobacter infections in humans. Plasmids, known as important mobile genetic elements, often carry genes for antibiotic resistance, virulence, and self-mobilization. They serve as the main vectors for transferring genetic material and spreading resistance and virulence among bacteria. In this study, we identified 34 new plasmids from 43 C. jejuni and C. coli strains isolated from retail meat using long-read and short-read genome sequencing. Pangenomic analysis of the plasmid assemblies and reference plasmids from GenBank revealed five distinct groups, namely, pTet, pVir, mega plasmids (>80 kb), mid plasmids (~30 kb), and small plasmids (<6 kb). Pangenomic analysis identified the core and accessory genes in each group, indicating a high degree of genetic similarity within groups and substantial diversity between the groups. The pTet plasmids were linked to tetracycline resistance phenotypes in host strains. The mega plasmids carry multiple genes (e.g., aph(3')-III, type IV and VI secretion systems, and type II toxin-antitoxin systems) important for plasmid mobilization, virulence, antibiotic resistance, and the persistence of Campylobacter. Together, the identification and comprehensive genetic characterization of new plasmids from Campylobacter food isolates contributes to understanding the mechanisms of gene transfer, particularly the spread of genetic determinants of virulence and antibiotic resistance in this important pathogen.},
}

@article {pmid39858487,
year = {2025},
author = {Tahmasebi, H and Arjmand, N and Monemi, M and Babaeizad, A and Alibabaei, F and Alibabaei, N and Bahar, A and Oksenych, V and Eslami, M},
title = {From Cure to Crisis: Understanding the Evolution of Antibiotic-Resistant Bacteria in Human Microbiota.},
journal = {Biomolecules},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/biom15010093},
pmid = {39858487},
issn = {2218-273X},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota/drug effects ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {The growing prevalence of antibiotic-resistant bacteria within the human microbiome has become a pressing global health crisis. While antibiotics have revolutionized medicine by significantly reducing mortality and enabling advanced medical interventions, their misuse and overuse have led to the emergence of resistant bacterial strains. Key resistance mechanisms include genetic mutations, horizontal gene transfer, and biofilm formation, with the human microbiota acting as a reservoir for antibiotic resistance genes (ARGs). Industrialization and environmental factors have exacerbated this issue, contributing to a rise in infections with multidrug-resistant (MDR) bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacteriaceae. These resistant pathogens compromise the effectiveness of essential treatments like surgical prophylaxis and chemotherapy, increase healthcare costs, and prolong hospital stays. This crisis highlights the need for a global One-Health approach, particularly in regions with weak regulatory frameworks. Innovative strategies, including next-generation sequencing (NGS) technologies, offer promising avenues for mitigating resistance. Addressing this challenge requires coordinated efforts, encompassing research, policymaking, public education, and antibiotic stewardship, to safeguard current antibiotics and foster the development of new therapeutic solutions. An integrated, multidimensional strategy is essential to tackle this escalating problem and ensure the sustainability of effective antimicrobial treatments.},
}

Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Microbiota/drug effects
Methicillin-Resistant Staphylococcus aureus/drug effects/genetics
Drug Resistance, Multiple, Bacterial/genetics
Bacteria/drug effects/genetics
Drug Resistance, Bacterial/genetics

@article {pmid39858396,
year = {2024},
author = {Dobrescu, MȘ and Țoc, DA and Pană, AG and Costache, C and Butiuc-Keul, A},
title = {The Difference a Year Can Make: How Antibiotic Resistance Mechanisms in Pseudomonas aeruginosa Have Changed in Northwestern Transylvania.},
journal = {Biomolecules},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/biom15010001},
pmid = {39858396},
issn = {2218-273X},
support = {13517/15446/03.10.2022//Babeș-Bolyai University/ ; },
mesh = {*Pseudomonas aeruginosa/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; Pseudomonas Infections/microbiology/drug therapy/epidemiology ; Romania/epidemiology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Integrons/genetics ; Drug Resistance, Bacterial/genetics ; beta-Lactamases/genetics/metabolism ; },
abstract = {This study examines the prevalence and the mechanisms of antibiotic resistance in Pseudomonas aeruginosa isolates collected from healthcare units in Northwestern Transylvania, Romania, between 2022 and 2023. Given the alarming rise in antibiotic resistance, the study screened 34 isolates for resistance to 10 antibiotics, 46 ARGs, and integrase genes using PCR analysis. The results reveal a concerning increase in multidrug-resistant (MDR) and extensively drug-resistant (XDR) isolates over the two-year period. Notably, the prevalence of ARGs encoding resistance to sulfonamides and beta-lactams, particularly sul1 and blaOXA-50, has shown a significant rise. Furthermore, the study detected the emergence of new resistance mechanisms in the same time interval. These include target protection and even more specific mechanisms, such as metallo-beta-lactamases or enzymes involved in the methylation of 23S rRNA. Statistical analysis further confirmed the correlation between Class I integrons and several ARGs, underscoring the role of horizontal gene transfer in the dissemination of resistance. These findings emphasize the urgent need for updated treatment strategies and monitoring programs to effectively combat the spread of ARGs in clinical settings.},
}

*Pseudomonas aeruginosa/drug effects/genetics
*Anti-Bacterial Agents/pharmacology
Humans
Pseudomonas Infections/microbiology/drug therapy/epidemiology
Romania/epidemiology
Drug Resistance, Multiple, Bacterial/genetics
Microbial Sensitivity Tests
Gene Transfer, Horizontal
Integrons/genetics
Drug Resistance, Bacterial/genetics
beta-Lactamases/genetics/metabolism

@article {pmid39858353,
year = {2025},
author = {Kløve, DC and Strube, ML and Heegaard, PMH and Astrup, LB},
title = {Mapping Antimicrobial Resistance in Staphylococcus epidermidis Isolates from Subclinical Mastitis in Danish Dairy Cows.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/antibiotics14010067},
pmid = {39858353},
issn = {2079-6382},
abstract = {Background/Objectives: Although Staphylococcus epidermidis is a key cause of subclinical mastitis in Danish dairy cows, its sensitivity to antimicrobials remains unexplored. Here, we analyzed sixty S. epidermidis isolates derived from 42 dairy cows across six conventional dairy herds in Denmark. Methods: Phenotypic resistance was measured by antimicrobial susceptibility testing and minimum inhibitory concentration (MIC) analysis, and genotypic resistance was examined through whole-genome sequencing and identification of antimicrobial resistance genes (ARGs). Correspondence between phenotypic and genotypic resistance was then evaluated by Cohen's kappa statistics. Furthermore, the presence of plasmid replicon genes and the strain diversity among the S. epidermidis isolates was investigated to associate these findings with the observed AMR patterns. Results: Results showed that 30/60 isolates (50.0%) were resistant to penicillin phenotypically, while 35/60 (58.3%) were positive for a corresponding blaZ gene (κ = 0.83, p < 0.01). A fosB gene, encoding fosfomycin resistance, was detected in all 60/60 isolates (100.0%), but fosfomycin resistance was not analyzed phenotypically. Based on MIC analysis, 3/60 isolates (5.0%) were multi-drug resistant, showing resistance towards penicillin, erythromycin, and tetracycline. However, in 11/60 genomes (18.3%), ARGs encoding resistance towards ≥3 antimicrobial classes (e.g., beta-lactams, phosphonic acid, tetracyclines, aminoglycosides, macrolides, lincosamides, and fusidane) were detected. Eleven different ARGs were detected among the 60 isolates in total. No methicillin-resistant Staphylococcus epidermidis (MRSE) were recorded. Results further showed that each herd had one primary sequence type (ST) and resistance profile associated with it, and plasmid-mediated horizontal gene transfer of ARGs was indicated This study underscores the importance of routine resistance surveillance and species-specific diagnoses to improve treatment outcomes and ensure prudent use of antimicrobials.},
}

@article {pmid39856955,
year = {2025},
author = {Zhang, Z and Zhao, H and Shi, C},
title = {Clonal Spread and Genetic Mechanisms Underpinning Ciprofloxacin Resistance in Salmonella enteritidis.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/foods14020289},
pmid = {39856955},
issn = {2304-8158},
support = {2024YFE0199000//National Key R&D Program of China/ ; 32202193//National Natural Science Foundation of China/ ; 32472458//National Natural Science Foundation of China/ ; },
abstract = {Salmonella enteritidis is a major cause of foodborne illness worldwide, and the emergence of ciprofloxacin-resistant strains poses a significant threat to food safety and public health. This study aimed to investigate the prevalence, spread, and mechanisms of ciprofloxacin resistance in S. enteritidis isolates from food and patient samples in Shanghai, China. A total of 1625 S. enteritidis isolates were screened, and 34 (2.1%) exhibited resistance to ciprofloxacin. Pulsed-field gel electrophoresis (PFGE) results suggested that clonal spread might have persisted among these 34 isolates in the local area for several years. Multiple plasmid-mediated quinolone resistance (PMQR) genes, GyrA mutations in the quinolone resistance-determining region (QRDR), and overexpression of RND efflux pumps were identified as potential contributors to ciprofloxacin resistance. PMQR genes oqxAB, qnrA, qnrB, and aac(6')-Ib-cr as well as GyrA mutations S83Y, S83R, D87Y, D87G, D87N, and S83Y-D87Y were identified. The co-transfer of the PMQR gene oqxAB with the ESBL gene blaCTX-M-14/55 on an IncHI2 plasmid with a size of ~245 kbp was observed through conjugation, highlighting the role of horizontal gene transfer in the dissemination of antibiotic resistance. Sequencing of the oqxAB-bearing plasmid p12519A revealed a 248,746 bp sequence with a typical IncHI2 backbone. A 53,104 bp multidrug resistance region (MRR) was identified, containing two key antibiotic resistance determinants: IS26-oqxR-oqxAB-IS26 and IS26-ΔISEcp1-blaCTX-M-14-IS903B. The findings of this study indicate that ciprofloxacin-resistant S. Enteritidis poses a significant threat to food safety and public health. The persistence of clonal spread and the horizontal transfer of resistance genes highlight the need for enhanced surveillance and control measures to prevent the further spread of antibiotic resistance.},
}

@article {pmid39855970,
year = {2025},
author = {Wang, D and Zhou, X and Fu, Q and Li, Y and Ni, BJ and Liu, X},
title = {Understanding bacterial ecology to combat antibiotic resistance dissemination.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2024.12.011},
pmid = {39855970},
issn = {1879-3096},
abstract = {The dissemination of antibiotic resistance from environmental sources is a growing concern. Despite the widespread occurrence of antibiotic resistance transmission events, there are actually multiple obstacles in the ecosystem that restrict the flow of bacteria and genes, in particular nonnegligible biological barriers. How these ecological factors help combat the dissemination of antibiotic resistance and relevant antibiotic resistance-diminishing organisms (ARDOs) deserves further exploration. This review summarizes the factors that influence the growth, metabolism, and environmental adaptation of antibiotic-resistant bacteria (ARB) and restrict the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Additionally, this review discusses the achievements in the application of ARDOs to improve biotechnology for wastewater and solid waste remediation while highlighting current challenges limiting their broader implementation.},
}

@article {pmid39854814,
year = {2025},
author = {Xu, Z and Li, S and Ma, Y and Li, C and Lu, H and Xiong, J and He, G and Li, R and Ren, X and Huang, B and Pan, X},
title = {Role of organophosphorus pesticides in facilitating plasmid-mediated conjugative transfer: Efficiency and mechanisms.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137318},
doi = {10.1016/j.jhazmat.2025.137318},
pmid = {39854814},
issn = {1873-3336},
abstract = {Non-antibiotic conditions, including organophosphorus pesticides (OPPs), have been implicated in the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) to varying degrees. While most studies focus on the toxicity of OPPs to humans and animals, their roles in ARG dissemination remain largely unexplored. In this study, we investigate the effects and involved molecular mechanisms of environmentally relevant concentrations of malathion and dimethoate, two representative OPPs, on plasmid-mediated conjugal transfer. By detecting reactive oxygen species (ROS) production and cell membrane permeability, we gained insights into the underlying processes. Furthermore, we substantiated the role of ROS and cell membrane permeability in plasmid-mediated conjugative transfer through the analysis of relevant antioxidant enzyme activities, cell membrane-related indices, and RNA sequences. Additionally, our examination of proton motive force and adenosine triphosphate content provided evidence that OPPs create conditions conducive to plasmid-mediated conjugative transfer from an energetic perspective. The findings of the present study highlight the potential risk of OPPs in promoting ARG spread, which could ultimately provide new theoretical support and direction for future research on the impacts of pesticides on ARG propagation.},
}

@article {pmid39852676,
year = {2025},
author = {Bukari, Z and Emmanuel, T and Woodward, J and Ferguson, R and Ezughara, M and Darga, N and Lopes, BS},
title = {The Global Challenge of Campylobacter: Antimicrobial Resistance and Emerging Intervention Strategies.},
journal = {Tropical medicine and infectious disease},
volume = {10},
number = {1},
pages = {},
doi = {10.3390/tropicalmed10010025},
pmid = {39852676},
issn = {2414-6366},
abstract = {Antimicrobial resistance (AMR) in Campylobacter species, particularly C. jejuni and C. coli, poses a significant public health threat. These bacteria, which are commonly found in livestock, poultry, companion animals, and wildlife, are the leading causes of foodborne illnesses, often transmitted through contaminated poultry. Extensive exposure to antibiotics in human and veterinary medicine creates selection pressure, driving resistance through mechanisms such as point mutations, horizontal gene transfer, and efflux pumps. Resistance to fluoroquinolones, macrolides, and tetracyclines complicates treatment and increases the risk of severe infections. Drug-resistant Campylobacter is transmitted to humans via contaminated food, water, and direct contact with animals, highlighting its zoonotic potential. Addressing this challenge requires effective interventions. Pre-harvest strategies like biosecurity and immune-based methods reduce bacterial loads on farms, while post-harvest measures, including carcass decontamination and freezing, limit contamination. Emerging approaches, such as bacteriocins and natural antimicrobials, offer chemical-free alternatives. Integrated, multidisciplinary interventions across the food chain are essential to mitigate AMR transmission and enhance food safety. Sustainable agricultural practices, antimicrobial stewardship, and innovative solutions are critical to curbing Campylobacter resistance and protecting global public health. Our review examines the dynamics of antimicrobial resistance in Campylobacter and presents current strategies to mitigate Campylobacter-related AMR, offering valuable insights for antimicrobial control in the poultry industry.},
}

@article {pmid39847570,
year = {2025},
author = {Al Sium, SM and Goswami, B and Chowdhury, SF and Naser, SR and Sarkar, MK and Faruq, MJ and Habib, MA and Akter, S and Banu, TA and Sarkar, MMH and Khan, MS},
title = {An insight into the genome-wide analysis of bacterial defense mechanisms in a uropathogenic Morganella morganii isolate from Bangladesh.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0313141},
pmid = {39847570},
issn = {1932-6203},
mesh = {*Morganella morganii/genetics/isolation & purification ; Bangladesh ; *Urinary Tract Infections/microbiology ; *Genome, Bacterial ; Humans ; *Phylogeny ; Genomic Islands/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The gram-negative, facultative anaerobic bacterium Morganella morganii is linked to a number of illnesses, including nosocomial infections and urinary tract infections (UTIs). A clinical isolate from a UTI patient in Bangladesh was subjected to high-throughput whole genome sequencing and extensive bioinformatics analysis in order to gather knowledge about the genomic basis of bacterial defenses and pathogenicity in M. morganii. With an average nucleotide identity (ANI) of more than 97% similarity to a reference genome and phylogenetic analysis verified the isolate as M. morganii. Genome annotation identified 3,718 protein-coding sequences, including genes for metabolism, protein processing, stress response, energy, and membrane transport. The presence of biosynthetic gene clusters points to the isolate's ability to create bioactive compounds, including antibiotics. Genomic islands contained genes for metal transporters, stress proteins, toxin proteins, and genes related to horizontal gene transfer. The beta-lactam resistance gene blaDHA was found using antimicrobial resistance (AMR) gene analysis across three databases. The virulence genes kdsA and cheY, which may be involved in chemotaxis and lipopolysaccharide production, were also available in the isolate, suggesting its high pathogenicity. The genome contained mobile genetic components and defense mechanisms, such as restriction modification and CRISPR-Cas systems, indicating the bacterium's ability to defend itself against viral attacks. This thorough investigation sheds important light on M. morganii's pathogenicity and adaptive tactics by revealing its genetic characteristics, AMR, virulence components, and defense mechanisms. For the development of targeted treatments and preventing the onset of resistance in clinical care, it is essential to comprehend these genetic fingerprints.},
}

*Morganella morganii/genetics/isolation & purification
Bangladesh
*Urinary Tract Infections/microbiology
*Genome, Bacterial
Humans
*Phylogeny
Genomic Islands/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid39846752,
year = {2025},
author = {McKeithen-Mead, S and Anderson, ME and García-Heredia, A and Grossman, AD},
title = {Activation and modulation of the host response to DNA damage by an integrative and conjugative element.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0046224},
doi = {10.1128/jb.00462-24},
pmid = {39846752},
issn = {1098-5530},
abstract = {Mobile genetic elements help drive horizontal gene transfer and bacterial evolution. Conjugative elements and temperate bacteriophages can be stably maintained in host cells. They can alter host physiology and regulatory responses and typically carry genes that are beneficial to their hosts. We found that ICEBs1, an integrative and conjugative element (ICE) of Bacillus subtilis, inhibits the host response to DNA damage (the SOS response). Activation of ICEBs1 before DNA damage reduced host cell lysis that was caused by SOS-mediated activation of two resident prophages. Further, activation of ICEBs1 itself activated the SOS response in a subpopulation of cells, and this activation was attenuated by the functions of the ICEBs1 genes ydcT and yddA (now ramT and ramA; ram for RecA modulator). Double-mutant analyses indicated that RamA functions to inhibit and RamT functions to both inhibit and activate the SOS response. Both RamT and RamA caused a reduction in RecA filaments, one of the early steps in activation of the SOS response. We suspect that there are several different mechanisms by which mobile genetic elements that generate single-stranded DNA (ssDNA) during their life cycle inhibit the host SOS response and RecA function, as RamT and RamA differ from the known SOS inhibitors encoded by conjugative elements.IMPORTANCEBacterial genomes typically contain mobile genetic elements, including bacteriophages (viruses) and integrative and conjugative elements, that affect host physiology. ICEs can excise from the chromosome and undergo rolling-circle replication, producing ssDNA, a signal that indicates DNA damage and activates the host SOS response. We found that following excision and replication, ICEBs1 of B. subtilis stimulates the host SOS response and that ICEBs1 encodes two proteins that limit the extent of this response. These proteins also reduce the amount of cell killing caused by resident prophages following their activation by DNA damage. These proteins are different from those previously characterized that inhibit the host SOS response and represent a new way in which ICEs can affect their host cells.},
}

@article {pmid39843582,
year = {2024},
author = {Silva, KPT and Khare, A},
title = {Antibiotic resistance mediated by gene amplifications.},
journal = {npj antimicrobials and resistance},
volume = {2},
number = {1},
pages = {35},
pmid = {39843582},
issn = {2731-8745},
support = {Intramural Research Program//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; Intramural Research Program//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Apart from horizontal gene transfer and sequence-altering mutational events, antibiotic resistance can emerge due to the formation of tandem repeats of genomic regions. This phenomenon, also known as gene amplification, has been implicated in antibiotic resistance in both laboratory and clinical scenarios, where the evolution of resistance via amplifications can affect treatment efficacy. Antibiotic resistance mediated by gene amplifications is unstable and consequently can be difficult to detect, due to amplification loss in the absence of the selective pressure of the antibiotic. Further, due to variable copy numbers in a population, amplifications result in heteroresistance, where only a subpopulation is resistant to an antibiotic. While gene amplifications typically lead to resistance by increasing the expression of resistance determinants due to the higher copy number, the underlying mechanisms of resistance are diverse. In this review article, we describe the various pathways by which gene amplifications cause antibiotic resistance, from efflux and modification of the antibiotic, to target modification and bypass. We also discuss how gene amplifications can engender resistance by alternate mutational outcomes such as altered regulation and protein structure, in addition to just an increase in copy number and expression. Understanding how amplifications contribute to bacterial survival following antibiotic exposure is critical to counter their role in the rise of antimicrobial resistance.},
}

@article {pmid39843314,
year = {2025},
author = {Yang, QE and Gao, JT and Zhou, SG and Walsh, TR},
title = {Cutting-edge tools for unveiling the dynamics of plasmid-host interactions.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.12.013},
pmid = {39843314},
issn = {1878-4380},
abstract = {The plasmid-mediated transfer of antibiotic resistance genes (ARGs) in complex microbiomes presents a significant global health challenge. This review examines recent technological advancements that have enabled us to move beyond the limitations of culture-dependent detection of conjugation and have enhanced our ability to track and understand the movement of ARGs in real-world scenarios. We critically assess the applications of single-cell sequencing, fluorescence-based techniques and advanced high-throughput chromatin conformation capture (Hi-C) approaches in elucidating plasmid-host interactions at unprecedented resolution. We also evaluate emerging techniques such as CRISPR-based phage engineering and discuss their potential for developing targeted strategies to curb ARG dissemination. Emerging data derived from these technologies have challenged our previous paradigms on plasmid-host compatibility and an awareness of an emerging uncharted realm for ARGs.},
}

@article {pmid39840972,
year = {2025},
author = {Zavan, L and Hor, L and Johnston, EL and Paxman, J and Heras, B and Kaparakis-Liaskos, M},
title = {Antigen 43 associated with Escherichia coli membrane vesicles contributes to bacterial cell association and biofilm formation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0189024},
doi = {10.1128/spectrum.01890-24},
pmid = {39840972},
issn = {2165-0497},
abstract = {Bacterial membrane vesicles (MVs) are produced by all bacteria and contribute to numerous bacterial functions due to their ability to package and transfer bacterial cargo. In doing so, MVs have been shown to facilitate horizontal gene transfer, mediate antimicrobial activity, and promote biofilm formation. Uropathogenic Escherichia coli is a pathogenic Gram-negative organism that persists in the urinary tract of its host due to its ability to form persistent, antibiotic-resistant biofilms. The formation of these biofilms is dependent upon proteins such as Antigen 43 (Ag43), which belongs to the widespread Autotransporter group of bacterial surface proteins. In E. coli, the autotransporter Ag43 has been shown to contribute to bacterial cell aggregation and biofilm formation via self-association of Ag43 between neighboring Ag43-expressing bacteria. As MVs package bacterial proteins, we investigated whether MVs produced by E. coli contained Ag43, and the ability of Ag43-expressing MVs to facilitate cell aggregation and biofilm formation. We showed that Ag43 expressing E. coli produced MVs that contained Ag43 on their surface and had an enhanced ability to bind to E. coli bacteria. Furthermore, we demonstrated that the addition of Ag43-containing MVs to Ag43-expressing E. coli significantly enhanced biofilm formation. These findings reveal the contribution of MVs harboring autotransporters in promoting bacterial aggregation and enhancing biofilm formation, highlighting the impact of MVs and their specific composition to bacterial adaptation and pathogenesis.IMPORTANCEAutotransporter proteins are the largest family of outer membrane and secreted proteins in Gram-negative bacteria which contribute to pathogenesis by promoting aggregation, biofilm formation, persistence, and cytotoxicity. Although the roles of bacterial autotransporters are well known, the ability of bacterial membrane vesicles (MVs) naturally released from the surface of bacteria to contain autotransporters and their role in promoting virulence remains less investigated. Our findings reveal that MVs produced by E. coli contain the autotransporter protein Ag43. Furthermore, we show that Ag43-containing MVs function to enhance bacterial cell interactions and biofilm formation. By demonstrating the ability of MVs to carry functional autotransporter adhesins, this work highlights the importance of MVs in disseminating autotransporters beyond the bacterial cell membrane to ultimately promote cellular interactions and enhance biofilm development. Overall, these findings have significant implications in furthering our understanding of the numerous ways in which MVs can facilitate bacterial persistence and pathogenesis.},
}

@article {pmid39837262,
year = {2025},
author = {Wang, Y and Liu, T and Sida, Y and Zhu, Y},
title = {Diversity and Evolution of the Mobilome Associated with Antibiotic Resistance Genes in Streptococcus anginosus.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1089/mdr.2024.0229},
pmid = {39837262},
issn = {1931-8448},
abstract = {Streptococcus anginosus is an important cause of pyogenic infections, bacteremia, and chronic maxillary sinusitis. Mobile genetic elements (MGEs) play a key role in lateral gene transfer, resulting in broad transfer of antibiotic resistance genes (ARGs). However, studies on ARG-associated MGEs in S. anginosus are still rare. To fill this gap, we used sequencing data from 11 clinical S. anginosus to characterize their mobilome diversity through comparative analysis. We found 47 well-characterized MGEs, including 23 putative integrative and conjugative elements (ICEs), 16 prophages/integrative mobilizable elements, and 8 composites. They were inserted into 16 positions, 4 of which were hot spots. A comprehensive analysis revealed that ARG-associated ICEs belong to four groups as follows: single serine integrases (ICESan49.2), tyrosine integrases (ICESan26.2), triple serine integrase ICEs (ICESan195.1), and a putative transposon integrase (ICESan49.1), all of which were similar to ICEs/transposons widely distributed among other streptococci. The eight composites were composed of multiple ICEs or transposons through successive accretion events (tandem or/and internal integration). In conclusion, we found that S. anginosus accumulates a variety of ARG-associated ICE/composites that may enable S. anginosus to serve as an ARG-associated MGE repository for other streptococci. The analysis of composites here provides a paradigm to further study mobilome evolution.},
}

@article {pmid39799916,
year = {2025},
author = {Li, Y and Liu, X and Guo, S and Wang, L and Tang, J},
title = {The combination of polystyrene microplastics and di (2-ethylhexyl) phthalate promotes the conjugative transfer of antibiotic resistance genes between bacteria.},
journal = {Ecotoxicology and environmental safety},
volume = {289},
number = {},
pages = {117681},
doi = {10.1016/j.ecoenv.2025.117681},
pmid = {39799916},
issn = {1090-2414},
mesh = {*Diethylhexyl Phthalate/toxicity ; *Microplastics/toxicity ; *Polystyrenes/toxicity ; *Plasticizers/toxicity ; Drug Resistance, Microbial/genetics ; Bacteria/drug effects/genetics ; Water Pollutants, Chemical/toxicity ; Gene Transfer, Horizontal ; Genes, Bacterial/drug effects ; },
abstract = {Plastic pollution has become a common phenomenon. The process of plastic degradation is accompanied by the release of microplastics and plasticizers. However, the coexistence of microplastics and plasticizers on the transfer of antibiotic resistance genes (ARGs) has not been reported until now. Here, polystyrene (PS) microplastics and plasticizer di (2-ethylhexyl) phthalate (DEHP) were used for combined treatment experiment and their effects and mechanisms on the transfer of ARGs between bacteria were explored. By increasing cell membrane permeability and the expression of correlated genes, the combined treatment group showed promoting effects on the transfer of ARGs than that of control, with the highest promoting effects observed at 1 mg/L PS and 0.1 mg/L DEHP, which was 3.0 times higher in ARGs transfer rate than that of control. It was found that PS and DEHP treatment alone also led to a higher conjugative transfer frequency, and the frequency of the combined treatment was lower than that of the corresponding single treatment group. This indicated that the effects of DEHP and microplastics on ARGs transfer might be antagonistic. Transcriptome analysis indicated that the transfer of ARGs affects bacterial ion binding, oxidative stress, and energy metabolism processes, while the expression of genes related to cell membrane permeability, DNA repair, bacterial drug resistance, and quorum sensing also increase. This study may provide new insights for explaining the combined effects of various pollutants in the environment on the spread of ARGs.},
}

*Diethylhexyl Phthalate/toxicity
*Microplastics/toxicity
*Polystyrenes/toxicity
*Plasticizers/toxicity
Drug Resistance, Microbial/genetics
Bacteria/drug effects/genetics
Water Pollutants, Chemical/toxicity
Gene Transfer, Horizontal
Genes, Bacterial/drug effects

@article {pmid39837038,
year = {2025},
author = {Zhao, M and Huang, K and Wen, F and Xia, H and Song, B},
title = {Biochar reduces plasmid-mediated antibiotic resistance gene transfer in earthworm ecological filters for rural sewage treatment.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137230},
doi = {10.1016/j.jhazmat.2025.137230},
pmid = {39837038},
issn = {1873-3336},
abstract = {The spread of antibiotic resistance genes (ARGs) in rural wastewater threatens both ecological environment and human health. Earthworm ecological filters (EEFs) represent a green technology for rural sewage treatment. However, their effectiveness in removing ARGs remains a significant challenge. This study aims to investigate the role and underlying mechanisms of biochar addition in enhancing ARGs removal in rural sewage using EEFs. To achieve this, the fate of chromosome- and plasmid-carried ARGs was quantified in constructed EEFs, both with and without biochar addition. The results showed that the biochar could effectively remove ARGs from rural sewage, with a better removal efficiency for plasmid-carried ARGs. The absolute abundance of plasmid-carried ARGs in the effluent was reduced by 0.4-11 times compared to chromosomal ones, showing removal stability improved by 13.11-74.51 %. Additionally, the functional microbial community attached on the high porosity of biochar surface promoted ARGs retention, increasing diffusion limitation in microbial assembly mechanisms by 4.61-29.44 %, which played a key role in plasmid-mediated horizontal gene transfer (HGT). Partial least squares structural equation modeling (PLS-SEM) revealed that biochar-mediated environmental changes and the HGT of mobile genetic elements (MGEs) were critical factors in reducing plasmid-carried ARGs in EEFs.},
}

@article {pmid39836086,
year = {2025},
author = {Xia, R and Yin, X and Balcazar, JL and Huang, D and Liao, J and Wang, D and Alvarez, PJJ and Yu, P},
title = {Bacterium-Phage Symbiosis Facilitates the Enrichment of Bacterial Pathogens and Antibiotic-Resistant Bacteria in the Plastisphere.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c08265},
pmid = {39836086},
issn = {1520-5851},
abstract = {The plastisphere, defined as the ecological niche for microbial colonization of plastic debris, has been recognized as a hotspot of pathogenic and antibiotic-resistant bacteria. However, the interactions between bacteria and phages facilitated by the plastisphere, as well as their impact on microbial risks to public health, remain unclear. Here, we analyzed public metagenomic data from 180 plastisphere and environmental samples, stemming from four different habitats and two plastic types (biodegradable and nonbiodegradable plastics) and obtained 611 nonredundant metagenome-assembled genomes (MAGs) and 4061 nonredundant phage contigs. The plastisphere phage community exhibited decreased diversity and virulent proportion compared to those found in environments. Indexes of phage-host interaction networks indicated significant associations of phages with pathogenic and antibiotic-resistant bacteria (ARB), particularly for biodegradable plastics. Known phage-encoded auxiliary metabolic genes (AMGs) were involved in nutrient metabolism, antibiotic production, quorum sensing, and biofilm formation in the plastisphere, which contributed to enhanced competition and survival of pathogens and ARB hosts. Phages also carried transcriptionally active virulence factor genes (VFGs) and antibiotic resistance genes (ARGs), and could mediate their horizontal transfer in microbial communities. Overall, these discoveries suggest that plastisphere phages form symbiotic relationships with their hosts, and that phages encoding AMGs and mediating horizontal gene transfer (HGT) could increase the source of pathogens and antibiotic resistance from the plastisphere.},
}

@article {pmid39833926,
year = {2025},
author = {Li, Z and Zhao, C and Mao, Z and Zhang, F and Dong, L and Song, C and Chen, Y and Fu, X and Ao, Z and Xiong, Y and Hui, Q and Song, W and Penttinen, P and Zhang, S},
title = {Structure and metabolic function of spatiotemporal pit mud microbiome.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {10},
pmid = {39833926},
issn = {2524-6372},
support = {2022HX04//Youth Fund of Postdoctor/ ; 2021JDJQ0038//Youth Fund of Sichuan Province/ ; },
abstract = {BACKGROUND: Pit mud (PM) hosts diverse microbial communities, which serve as a medium to impart flavor and quality to Baijiu and exhibit long-term tolerance to ethanol and acids, resulting in a unique ecosystem. However, the ecology and metabolic functions of PM remain poorly understood, as many taxa in PM represent largely novel lineages. In this study, we used a combination of metagenomic analysis and chemical derivatization LC-MS analysis to provide a comprehensive overview of microbial community structure, metabolic function, phylogeny, horizontal gene transfer, and the relationship with carboxyl compounds in spatiotemporal PM samples.

RESULTS: Our findings revealed three distinct stages in the spatiotemporal changes of prokaryotic communities in PM: an initial phase dominated by Lactobacillus, a transitional phase, and a final state of equilibrium. Significant variations in α- and β-diversity were observed across different spatial and temporal PM samples. We identified 178 medium- and high-quality non-redundant metagenome-assembled genomes (MAGs), and constructed their phylogenetic tree, depicting their roles in the carbon, nitrogen, and sulfur cycles. The Wood-Ljungdahl pathway and reverse TCA cycle were identified as the main carbon fixation mechanisms, with both hydrogenotrophic and aceticlastic methanogens playing a major role in methane production, and methylotrophic pathway observed in older PM. Furthermore, we identified relationships between prokaryotes and 29 carboxyl metabolites, including medium- and long-chain fatty acids. Horizontal gene transfer (HGT) was widespread in PM, particularly among clostridia, Bacteroidota, Bacilli, and Euryarchaeota, and was shown to play critical roles in fermentation dynamics, carbon fixation, methane production, and nitrogen and sulfur metabolism.

CONCLUSION: Our study provides new insights into the evolution and function of spatiotemporal PM, as well as its interactions with carboxyl metabolites. Lactobacillus dominated in new PM, while methanogens and clostridia were predominant in older or deeper PM layers. The three distinct stages of prokaryotic community development in PM and HGT played critical roles in metabolic function of spatiotemporal PM. Furthermore, this study highlights the importance of α-diversity, β-diversity, methanogens, and Clostridium as useful indicators for assessing PM quality in the production of high-quality Baijiu.},
}

@article {pmid39829789,
year = {2025},
author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Swartz, M and Wadsworth, CB},
title = {Re-visiting the potential impact of doxycycline post-exposure prophylaxis (doxy-PEP) on the selection of doxycycline resistance in Neisseria commensals.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.09.632169},
pmid = {39829789},
issn = {2692-8205},
abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) is a preventative strategy demonstrated to reduce bacterial sexually transmitted infections in high-risk populations. However, the impact of doxy-PEP on antibiotic resistance acquisition in key members of our microbiomes, is as of yet unclear. For example, commensal Neisseria are known reservoirs of resistance for gonococci through horizontal gene transfer (HGT), and are more likely to experience bystander selection due to doxy-PEP as they are universally carried. Thus, the consequences of doxycycline selection on commensal Neisseria will be critical to investigate to understand possible resistance mechanisms that may be transferred to an important human pathogen. Here, we use in vitro antibiotic gradients to evolve four Neisseria commensals (N. cinerea, N. canis, N. elongata, and N. subflava, n=4 per species) across a 20-day time course; and use whole genome sequencing to nominate derived mutations. After selection, 12 of 16 replicates evolved doxycycline resistance (> 1 μg/mL). Across resistant lineages: An A46T substitution in the repressor of the Mtr efflux pump (MtrR) and a V57M substitution in the 30 ribosomal protein S10 were clearly associated with elevated MICs. Additional mutations in ribosomal components also emerged in strains with high MICs (i.e., 16S rRNA G1057C , RplX A14T). We find the MtrR 46T, RpsJ 57M, and RplX 14T circulating in natural commensal populations. Furthermore, in vitro co-evolution of N. gonorrhoeae with Neisseria commensals demonstrated rapid transfer of the pConj plasmid to N. subflava and N. cinerea , and p bla to N. cinerea . Finally, collection of novel commensals from human hosts reveals 46% of isolates carrying doxycycline resistance; and doxycycline resistance was significantly greater in participants self-reporting doxycycline use in the past 6 months. High-level doxycycline resistance (> 8 μg/mL) was always associated with carriage of the ribosomal protection protein (tetM) and pConj. Ultimately, characterizing the contemporary prevalence of doxycycline resistance, and underlying resistance mechanisms, in commensal communities may help us to predict the long-term impact of doxy-PEP on Neisseria , and the likelihood of transferring particular genotypes across species' boundaries.},
}

@article {pmid39827804,
year = {2025},
author = {Ye, T and Li, Y and Zhou, X and Ye, Y and Liu, X and Xiong, W},
title = {Hormesis-like effects of black phosphorus nanosheets on the spread of multiple antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137207},
doi = {10.1016/j.jhazmat.2025.137207},
pmid = {39827804},
issn = {1873-3336},
abstract = {The production scalability and increasing demand for black phosphorus nanosheets (BPNSs) inevitably lead to environmental leakage. Although BPNSs' ecotoxicological effects have been demonstrated, their indirect health risks, such as inducing increased resistance in pathogenic bacteria, are often overlooked. This study explores the influence of BPNSs on the horizontal gene transfer of antibiotic resistance genes (ARGs) facilitated by the RP4 plasmid, which carries multiple resistance genes. The results indicated that BPNSs exhibited concentration-dependent hormesis-like effects on bacterial conjugation gene transfer. Specifically, at sub-inhibitory concentrations (0.0001-1 mg/L), BPNSs promoted both intra- and intergeneric conjugative transfer, demonstrating an initial increase followed by a decline, with transfer rates rising by 1.5-3.1-fold and 1.5-3.3-fold, respectively. BPNSs were found to induce reactive oxygen species (ROS) production, increase malondialdehyde levels, and trigger the SOS response, enhancing plasmid uptake. Additionally, BPNSs increased membrane permeability by forming pores and upregulating outer membrane porins (OMPs) genes. At higher BPNSs concentrations (0.1-1 mg/L), conjugative frequency was inhibited due to the disruption of the cellular antioxidant system and changes in the adsorption process. These findings underscore the influence of BPNSs on the conjugative transfer of ARGs, complementing current knowledge of the biotoxicity and potential ecological risks associated with BPNSs.},
}

@article {pmid39529437,
year = {2025},
author = {Curtsinger, HD and Martínez-Absalón, S and Liu, Y and Lopatkin, AJ},
title = {The metabolic burden associated with plasmid acquisition: An assessment of the unrecognized benefits to host cells.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {47},
number = {2},
pages = {e2400164},
doi = {10.1002/bies.202400164},
pmid = {39529437},
issn = {1521-1878},
support = {1R35GM150871-01 (AJL)/GM/NIGMS NIH HHS/United States ; },
mesh = {*Plasmids/genetics/metabolism ; Humans ; *Conjugation, Genetic ; *Bacteria/metabolism/genetics ; Gene Transfer, Horizontal ; },
abstract = {Bacterial conjugation, wherein DNA is transferred between cells through direct contact, is highly prevalent in complex microbial communities and is responsible for spreading myriad genes related to human and environmental health. Despite their importance, much remains unknown regarding the mechanisms driving the spread and persistence of these plasmids in situ. Studies have demonstrated that transferring, acquiring, and maintaining a plasmid imposes a significant metabolic burden on the host. Simultaneously, emerging evidence suggests that the presence of a conjugative plasmid can also provide both obvious and unexpected benefits to their host and local community. Combined, this highlights a continuous cost-benefit tradeoff at the population level, likely contributing to overall plasmid abundance and long-term persistence. Yet, while the metabolic burdens of plasmid conjugation, and their causes, are widely studied, their attendant potential advantages are less clear. Here, we summarize current perspectives on conjugative plasmids' metabolic burden and then highlight the lesser-appreciated yet critical benefits that plasmid-mediated metabolic burdens may provide. We argue that this largely unexplored tradeoff is critical to both a fundamental theory of microbial populations and engineering applications and therefore warrants further detailed study.},
}

*Plasmids/genetics/metabolism
Humans
*Conjugation, Genetic
*Bacteria/metabolism/genetics
Gene Transfer, Horizontal

@article {pmid39826759,
year = {2025},
author = {Wang, C and Yin, X and Xu, X and Wang, D and Wang, Y and Zhang, T},
title = {Antibiotic resistance genes in anaerobic digestion: Unresolved challenges and potential solutions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132075},
doi = {10.1016/j.biortech.2025.132075},
pmid = {39826759},
issn = {1873-2976},
abstract = {Antimicrobial resistance (AMR) threatens public health, necessitating urgent efforts to mitigate the global impact of antibiotic resistance genes (ARGs). Anaerobic digestion (AD), known for volatile solid reduction and energy generation, also presents a feasible approach for the removal of ARGs. This review encapsulates the existing understanding of ARGs and antibiotic-resistant bacteria (ARB) during the AD process, highlighting unresolved challenges pertaining to their detection and quantification. The questions raised and discussed include: Do current ARGs detection methods meet qualitative and quantitative control requirements? How can we conduct risk assessments of ARGs? What happens to ARGs when they come into co-exposure with other emerging pollutants? How can the application of internal standards bolster the reliability of the AD resistome study? What are the potential future research directions that could enhance ARG elimination? Investigating these subjects will assist in shaping more efficient management strategies that employ AD for effective ARG control.},
}

@article {pmid39826720,
year = {2025},
author = {Akhoon, BA and Qiao, Q and Stewart, A and Chen, J and Rodriguez Lopez, CM and Corbin, KR},
title = {Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {139980},
doi = {10.1016/j.ijbiomac.2025.139980},
pmid = {39826720},
issn = {1879-0003},
abstract = {Bacterial cellulose (BC) holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges in bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer (HGT) in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters (BGCs), including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.},
}

@article {pmid39826554,
year = {2025},
author = {Kirsch, R and Okamura, Y and García-Lozano, M and Weiss, B and Keller, J and Vogel, H and Fukumori, K and Fukatsu, T and Konstantinov, AS and Montagna, M and Moseyko, AG and Riley, EG and Slipinski, A and Vencl, FV and Windsor, DM and Salem, H and Kaltenpoth, M and Pauchet, Y},
title = {Symbiosis and horizontal gene transfer promote herbivory in the megadiverse leaf beetles.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.12.028},
pmid = {39826554},
issn = {1879-0445},
abstract = {Beetles that feed on the nutritionally depauperate and recalcitrant tissues provided by the leaves, stems, and roots of living plants comprise one-quarter of herbivorous insect species. Among the key adaptations for herbivory are plant cell wall-degrading enzymes (PCWDEs) that break down the fastidious polymers in the cell wall and grant access to the nutritious cell content. While largely absent from the non-herbivorous ancestors of beetles, such PCWDEs were occasionally acquired via horizontal gene transfer (HGT) or by the uptake of digestive symbionts. However, the macroevolutionary dynamics of PCWDEs and their impact on evolutionary transitions in herbivorous insects remained poorly understood. Through genomic and transcriptomic analyses of 74 leaf beetle species and 50 symbionts, we show that multiple independent events of microbe-to-beetle HGT and specialized symbioses drove convergent evolutionary innovations in approximately 21,000 and 13,500 leaf beetle species, respectively. Enzymatic assays indicate that these events significantly expanded the beetles' digestive repertoires and thereby contributed to their adaptation and diversification. Our results exemplify how recurring HGT and symbiont acquisition catalyzed digestive and nutritional adaptations to herbivory and thereby contributed to the evolutionary success of a megadiverse insect taxon.},
}

@article {pmid39824780,
year = {2025},
author = {Wu, X and Peng, J and Malik, AA and Peng, Z and Luo, Y and Fan, F and Lu, Y and Wei, G and Delgado-Baquerizo, M and Liesack, W and Jiao, S},
title = {A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria.},
journal = {Ecology letters},
volume = {28},
number = {1},
pages = {e70064},
doi = {10.1111/ele.70064},
pmid = {39824780},
issn = {1461-0248},
support = {42122050//National Science Foundation for Excellent Young Scholars of China/ ; 42277307 & 41977038//National Natural Science Foundation of China/ ; 2021YFD1900500//National Key Research and Development Program of China/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Bacteria/metabolism/genetics ; *Genome, Bacterial ; *Genome Size ; Gene Transfer, Horizontal ; Microbiota ; Biomass ; },
abstract = {Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between carbon metabolic strategies and genomic traits like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis of 2650 genomes, integrated whole-genome sequencing data, and performed a continental-scale metagenomic field study. We found that genome size was tightly associated with an increase in the ratio between genes encoding for polysaccharide decomposition and biomass synthesis that we defined as the carbon acquisition-to-biomass yield ratio (A/Y). We also show that horizontal gene transfer played a major evolutionary role in the expanded bacterial capacities in carbon acquisition. Our continental-scale field study further revealed a significantly negative relationship between the A/Y ratio and soil organic carbon stocks. Our work demonstrates a global relationship between genome size and the encoded carbon metabolic strategies of soil bacteria across terrestrial microbiomes.},
}

*Soil Microbiology
*Carbon/metabolism
*Bacteria/metabolism/genetics
*Genome, Bacterial
*Genome Size
Gene Transfer, Horizontal
Microbiota
Biomass

@article {pmid39824112,
year = {2025},
author = {Farooq, A and Rafique, A and Han, E and Park, SM},
title = {Global dissemination of the beta-lactam resistance gene blaTEM-1 among pathogenic bacteria.},
journal = {The Science of the total environment},
volume = {963},
number = {},
pages = {178521},
doi = {10.1016/j.scitotenv.2025.178521},
pmid = {39824112},
issn = {1879-1026},
abstract = {Antibiotic resistance presents a burgeoning global health crisis, with over 70 % of pathogenic bacteria now exhibiting resistance to at least one antibiotic. This study leverages a vast dataset of 618,853 pathogenic bacterial genomes from the NCBI pathogen detection database, offering comprehensive insights into antibiotic resistance patterns, species-specific profiles, and transmission dynamics of resistant pathogens. We centered our investigation on the beta-lactam resistance gene blaTEM-1, found in 43,339 genomes, revealing its extensive distribution across diverse species and isolation sources. The study unveiled the prevalence of 15 prominent antibiotic resistance genes (ARGs), including those conferring resistance to beta-lactam, aminoglycoside, and tetracycline antibiotics. Distinct resistance patterns were observed between Gram-positive and Gram-negative bacteria, indicating the influence of phylogeny on resistance dissemination. Notably, the blaTEM-1 gene demonstrated substantial prevalence across a wide array of bacterial species (8) and a high number of isolation sources (11). Genetic context analysis revealed associations between blaTEM-1 and mobile genetic elements (MGEs) like transposons and insertion sequences. Additionally, we observed recent horizontal transfer events involving clusters of blaTEM-1 genes and MGEs underscore the potential of MGEs in facilitating the mobilization of ARGs. Our findings underscore the importance of adopting a One Health approach to global genomic pathogen surveillance, aiming to uncover the transmission routes of ARGs and formulate strategies to address the escalating antibiotic resistance crisis.},
}

@article {pmid39824023,
year = {2025},
author = {Guo, X and Yu, P and Guo, J and Zhao, HP and Lai, CY},
title = {Viral auxiliary roles in hydrolytic and biosynthetic metabolism regulate prokaryotic microbial interactions in anaerobic digestion.},
journal = {Water research},
volume = {274},
number = {},
pages = {123140},
doi = {10.1016/j.watres.2025.123140},
pmid = {39824023},
issn = {1879-2448},
abstract = {Anaerobic digestion (AD) viruses have gained recognition as significant regulators of microbial interactions within AD communities, yet their ecological roles remain largely unexplored. In this study, we investigated the ecological roles of AD viruses in regulating microbial interactions among syntrophic hosts. We recovered 3921 diverse viral sequences from four full-scale anaerobic digesters and confirmed their widespread presence across 127 global metagenomic sampling sites (with >95 % sequence similarity), underscoring the ubiquity of prokaryotic viruses in AD-related systems. Through the construction of virus-prokaryote interactions (66.8 % validated at the transcriptional level) and analysis of viral-host transcriptional abundances, we identified significant associations between AD viruses and key processes, including hydrolysis, acidogenesis, and methanogenesis. Notably, polyvalent viruses were found to interact with both hydrolytic and fermentative communities. We further characterized viral auxiliary metabolism, hydrolytic substrate spectra, and microbial auxotrophy, showing that viruses not only could enhance the breakdown of complex substrates (e.g., cellulose, chitin, peptidoglycan) but also potentially supported the biosynthesis of essential nutrients (e.g., cysteine, methionine, heme, and cobalamin). These activities were proposed to regulate resource fluxes through alternating lysogenic and lytic cycles. Phylogenetic analysis of viral gene and horizontal gene transfer (HGT) identification suggest that AD viruses employ promiscuous infection on syntrophic hosts, potentially as an adaptive evolutionary strategy in the AD ecosystem. This study provides new insights into the ecological roles of AD viruses, highlighting their potential impact on the stability and functionality of AD systems.},
}

@article {pmid39823837,
year = {2025},
author = {Zhang, S and Ye, Q and Wang, M and Zhu, D and Jia, R and Chen, S and Liu, M and Yang, Q and Zhao, X and Wu, Y and Huang, J and Ou, X and Sun, D and Tian, B and He, Y and Wu, Z and Cheng, A},
title = {Isolation and characterization of a broad-spectrum bacteriophage against multi-drug resistant Escherichia coli from waterfowl field.},
journal = {Poultry science},
volume = {104},
number = {2},
pages = {104787},
doi = {10.1016/j.psj.2025.104787},
pmid = {39823837},
issn = {1525-3171},
abstract = {Escherichia coli (E. coli) is a significant pathogen responsible for intestinal infections and foodborne diseases. The rise of antibiotic resistance poses a significant challenge to global public health. Traditional antibiotic therapy is becoming increasingly ineffective, highlighting the urgent need for innovative control strategies. This study explores the potential of bacteriophages as a sustainable alternative to traditional antibiotics. From 2021 to 2022, a total of 183 non-repetitive duck source fecal samples were collected from Mianyang City, Sichuan Province, and 126 strains of E. coli were isolated. The minimum inhibitory concentration (MIC) test showed that these strains exhibited high resistance to piperacillin (96.8%), tetracycline (88.9%), and chloramphenicol (86.5%). It is concerning that 93.7% of the isolates are classified as multidrug-resistant (MDR), posing a significant threat to existing treatment options. 20 bacteriophages were isolated from fecal and soil samples, among which 5 bacteriophages were selected for further analysis. Bacteriophage YP6 showed excellent lytic effects on MDR strains, especially strain MY104, as well as representative serotypes O1 (E. coli MY51) and O18 (E. coli MY106). The identification of YP6 as a member of the Myoviridae family was conducted using transmission electron microscopy, and it was found to have an optimal infection factor of 0.1. Bacteriophages exhibit significant thermal and pH stability, maintaining survival at temperatures up to 60 °C and pH ranges of 4 to 10. Whole genome sequencing confirmed that YP6 has a double stranded DNA genome of 139,323 base pairs (bp), and no antibiotic resistance or virulence genes were found, indicating a low possibility of horizontal gene transfer. In addition, YP6 effectively inhibits the formation of E. coli biofilm, which is a key factor in chronic infections. The in vivo experiments using Galleria mellonella (G. mellonella) larvae have shown that it has a significant protective effect against MDR E. coli infection. In summary, bacteriophage YP6 is expected to become a therapeutic agent against MDR E. coli infection due to its broad host range, environmental stability, and biofilm inhibition properties. Future research should optimize bacteriophage preparations, evaluate the safety and efficacy of animal models, and establish clinical application plans in the field of food safety.},
}

@article {pmid39818750,
year = {2025},
author = {Shao, D and Ju, X and Wu, Y and Zhang, Y and Yan, Z and Li, Y and Wang, L and Parkhill, J and Walsh, TR and Wu, C and Shen, J and Wang, Y and Zhang, R and Shen, Y},
title = {Quaternary Ammonium Compounds: A New Driver and Hidden Threat for mcr-1 Prevalence in Hospital Wastewater and Human Feces.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c11368},
pmid = {39818750},
issn = {1520-5851},
abstract = {The emergence of mobile colistin resistance gene mcr-1 has attracted global attention. The prevalence of mcr-1-positive Escherichia coli (MCRPEC) in humans largely decreased following the ban of colistin as an animal growth promoter in China. However, the prevalence of MCRPEC in the hospital environment and the relationship between disinfectants and mcr-1 remain unclear. We found that MCRPEC prevalence was low in the feces of healthy humans attending physical examinations in six hospitals (4.6%, 71/1532) but high in hospital wastewater (50.0%, 27/54). mcr-1 was mainly located on IncI2 (63.0% in wastewater and 62.0% in feces) and IncHI2 plasmids (18.5% in wastewater and 21.1% in feces). High similarity of the mcr-1 context and its carrying plasmids was observed in human and wastewater MCRPEC, with several isolates clustering together. The coexistence of the ESBL gene blaCTX-M with mcr-1 occurred in 19.7% of IncI2 plasmids. Notably, 60.0% of IncHI2 plasmids exhibited co-occurrence of mcr-1 with the disinfectant resistance gene (DRG) qacEΔ1, conferring resistance to quaternary ammonium compounds (QACs). We revealed that QACs, rather than the other two types of disinfectants─ortho-phthalaldehyde (OPA) and povidone-iodine (PVP-I)─select for plasmids carrying both qacEΔ1 and mcr-1 and elevate their conjugative transfer frequency. Monitoring of DRGs in MCRPEC and managing disinfectant use are urgently needed in healthcare settings to mitigate the spread of colistin resistance from hospital environments to inpatients.},
}

@article {pmid39817515,
year = {2025},
author = {Djordjevic, M and Zivkovic, L and Ou, HY and Djordjevic, M},
title = {Nonlinear regulatory dynamics of bacterial restriction-modification systems modulates horizontal gene transfer susceptibility.},
journal = {Nucleic acids research},
volume = {53},
number = {2},
pages = {},
pmid = {39817515},
issn = {1362-4962},
support = {7750294//Science Fund of the Republic of Serbia/ ; //Ministry of Science and Technological Development of the Republic of Serbia/ ; 32370186//National Natural Science Foundation of China/ ; },
mesh = {*Gene Transfer, Horizontal ; *DNA Restriction-Modification Enzymes/genetics ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Nonlinear Dynamics ; Models, Genetic ; Bacteria/genetics ; Plasmids/genetics ; },
abstract = {Type II restriction-modification (R-M) systems play a pivotal role in bacterial defense against invading DNA, influencing the spread of pathogenic traits. These systems often involve coordinated expression of a regulatory protein (C) with restriction (R) enzymes, employing complex feedback loops for regulation. Recent studies highlight the crucial balance between R and M enzymes in controlling horizontal gene transfer (HGT). This manuscript introduces a mathematical model reflecting R-M system dynamics, informed by biophysical evidence, to minimize reliance on arbitrary parameters. Our analysis clarifies the observed variations in M-to-R ratios, emphasizing the regulatory role of the C protein. We analytically derived a stability diagram for C-regulated R-M systems, offering a more straightforward analysis method over traditional numerical approaches. Our findings reveal conditions leading to both monostability and bistability, linking changes in the M-to-R ratio to factors like cell division timing and plasmid replication rates. These variations may link adjusting defense against phage infection, or the acquisition of new genes such as antibiotic resistance determinants, to changing physiological conditions. We also performed stochastic simulations to show that system regulation may significantly increase M-to-R ratio variability, providing an additional mechanism to generate heterogeneity in bacterial population.},
}

*Gene Transfer, Horizontal
*DNA Restriction-Modification Enzymes/genetics
Bacterial Proteins/genetics/metabolism
Gene Expression Regulation, Bacterial
Nonlinear Dynamics
Models, Genetic
Bacteria/genetics
Plasmids/genetics

@article {pmid39816412,
year = {2022},
author = {Arredondo-Hernandez, R and Siebe, C and Castillo-Rojas, G and Ponce de León, S and López-Vidal, Y},
title = {The synergistic interaction of systemic inflammation, dysbiosis and antimicrobial resistance promotes growth restriction in children with acute severe malnutrition: An emphasis on Escherichia coli.},
journal = {Frontiers in antibiotics},
volume = {1},
number = {},
pages = {1001717},
pmid = {39816412},
issn = {2813-2467},
abstract = {A healthy development is denied to millions of children worldwide as harsh life conditions manifest themselves in an altered inflammation-prone microbiome crosstalk environment. Keynote of this tragedy is that insufficient nutritious amino acid blocks lipids-intake to sustain diverse microbiota, and promotes the generalist strategy followed by Escherichia coli -besides other proteobacteria- of shifting gut metabolism, subverting the site specificity of first immune reaction. Furthermore, it could be hypothesized that selective success lies in their ability to induce inflammation, since this phenomenon also fuels horizontal gene transfer (HGT). In this review, we dilucidate how immune mechanisms of environmental enteric dysfunction affect overgrowth restriction, infectious morbidity rate, and acquired lifelong risks among severe acute malnourished children. Also, despite acknowledging complexities of antimicrobial resistant enrichment, we explore and speculate over the links between virulence regulation and HGT as an indissociable part in the quest for new inflammatory niches by open genome bacteria, particularly when both collide in the most vulnerable.},
}

@article {pmid39813956,
year = {2025},
author = {Yang, QE and Lin, Z and Gan, D and Li, M and Liu, X and Zhou, S and Walsh, TR},
title = {Microplastics mediates the spread of antimicrobial resistance plasmids via modulating conjugal gene expression.},
journal = {Environment international},
volume = {195},
number = {},
pages = {109261},
doi = {10.1016/j.envint.2025.109261},
pmid = {39813956},
issn = {1873-6750},
abstract = {Antimicrobial resistance (AMR) and environmental degradation are existential global public health threats. Linking microplastics (MPs) and AMR is particularly concerning as MPs pollution would have significant ramifications on controlling of AMR; however, the effects of MPs on the spread and genetic mechanisms of AMR bacteria remain unclear. Herein, we performed Simonsen end-point conjugation to investigate the impact of four commonly used MPs on transfer of clinically relevant plasmids. The transfer breadth of a representative pA/C_MCR-8 plasmid across bacterial communities was confirmed by the cell sorting and 16S rRNA gene amplicon sequencing. Our study shows that exposure to four commonly found MPs promotes the conjugation rates of four clinically relevant AMR plasmids by up to 200-fold, when compared to the non-exposed group and that the transfer rates are MP concentrations demonstrate a positive correlation with higher transfer rates. Furthermore, we show that MPs induce the expression of plasmid-borne conjugal genes and SOS-linked genes such as recA, lexA, dinB and dinD. High-throughput sequencing of the broad transmission of plasmid pA/C_MCR-8, shows distribution over two main phyla, Pseudomonadota (50.0 %-95.0 %) and Bacillota (0.4 %-2.0 %). These findings definitively link two global health emergencies - AMR and environmental degradation via MPs, and to tackle global AMR, we must also now consider plastic utilisation and waste management.},
}

@article {pmid39807864,
year = {2025},
author = {Nakatsu, G and Ko, D and Michaud, M and Franzosa, EA and Morgan, XC and Huttenhower, C and Garrett, WS},
title = {Virulence factor discovery identifies associations between the Fic gene family and Fap2[+] fusobacteria in colorectal cancer microbiomes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0373224},
doi = {10.1128/mbio.03732-24},
pmid = {39807864},
issn = {2150-7511},
abstract = {Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2[+] Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2[+] Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants. Taken together, our study uncovers Fic genes as potential virulence factors in Fap2[+] fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.},
}

@article {pmid39805347,
year = {2025},
author = {Sasikumar, J and Shaikh, HA and Naik, B and Laha, S and Das, SP},
title = {Emergence of fungal hybrids - Potential threat to humans.},
journal = {Microbial pathogenesis},
volume = {200},
number = {},
pages = {107278},
doi = {10.1016/j.micpath.2025.107278},
pmid = {39805347},
issn = {1096-1208},
abstract = {Fungal hybrids arise through the interbreeding of distinct species. This hybridization process fosters increased genetic diversity and the emergence of new traits. Mechanisms driving hybridization include the loss of heterozygosity, copy number variations, and horizontal gene transfer. Genetic mating barriers, changes in ploidy, chromosomal instability, and genomic diversity influence hybridization. These factors directly impact the fitness and adaptation of hybrid offspring. Epigenetic factors, including DNA methylation, histone modifications, non-coding RNAs, and chromatin remodelling, play a role in post-mating isolation in hybrids. In addition to all these mechanisms, successful hybridization in fungi is ensured by cellular mechanisms like mitochondrial inheritance, transposable elements, and other genome conversion mechanisms. These mechanisms support hybrid life and enhance the virulence and pathogenicity of fungal hybrids, which provoke diseases in host organisms. Recent advancements in sequencing have uncovered fungal hybrids in pathogens like Aspergillus, Candida, and Cryptococcus. Examples of these hybrids, such as Aspergillus latus, Candida metapsilosis, and Cryptococcus neoformans, induce severe human infections. Identifying fungal hybrids is challenging due to their altered genome traits. ITS sequencing has emerged as a promising method for diagnosing these hybrids. To prevent the emergence of novel hybrid fungal pathogens, it is crucial to develop effective diagnostic techniques and closely monitor pathogenic fungal populations for signs of hybridization. This comprehensive review delves into various facts about fungal hybridization, including its causes, genetic outcomes, barriers, diagnostic strategies, and examples of emerging fungal hybrids. The review emphasises the potential threat that fungal hybrids pose to human health and highlights their clinical significance.},
}

@article {pmid39803089,
year = {2024},
author = {Yadav, KS and Pawar, S and Datkhile, K and Patil, SR},
title = {Study on the Mobile Colistin Resistance (mcr-1) Gene in Gram-Negative Bacilli in a Rural Tertiary Care Hospital in Western Maharashtra.},
journal = {Cureus},
volume = {16},
number = {12},
pages = {e75569},
pmid = {39803089},
issn = {2168-8184},
abstract = {BACKGROUND: Colistin, a last-resort antibiotic for treating multidrug-resistant Gram-negative bacterial infections, has increased resistance as a result of the emergence of the mcr-1 gene. The mcr-1gene, which confers colistin resistance, is often carried on plasmids, facilitating its spread by horizontal gene transfer among bacterial populations. The rising prevalence of mcr-1-mediated resistance poses significant challenges for infection control and treatment efficacy. This study aimed to detect and investigate the prevalence of the mcr-1 gene among Gram-negative bacilli isolated from clinical specimens in a rural tertiary care hospital and to analyze the plasmid-mediated mechanisms of colistin resistance.

MATERIALS AND METHODS: A cross-sectional study was conducted over two years at Krishna Institute of Medical Sciences, Karad. Gram-negative bacilli were isolated from clinical specimens and identified using standard methodology. Antimicrobial susceptibility testing was performed by using the Vitek-2 Compact (bioMerieux, Marcy-l'Étoile, France) method and the colistin-resistance broth microdilution method (BMD). Polymerase chain reaction (PCR) was done for the presence of mcr-1 gene in colistin-resistant isolates.

RESULTS: Out of 359 Gram-negative bacilli isolates, 93 (25.90%) demonstrated resistance to colistin. Among these resistant strains, the mcr-1 gene was identified in 13 (13.97%) of the isolates. The gene was predominantly found in Pseudomonas aeruginosa (8, 61.53%), followed by Klebsiella pneumoniae (3, 23.07%), Acinetobacter baumannii (2, 15.38%) among the 13 isolates. Out of the various specimens received, mcr-1 gene was found in endotracheal tube (4, 30.76%), urine (4, 30.76%), pus (3, 23.07%), sputum (1, 7.69%), and blood (1, 7.69%). Colistin minimum inhibitory concentration (MIC) value for these resistant isolates ranged from 4 to 16 µg/ml.

CONCLUSION: The study highlights a significant prevalence of mcr-1 plasmid-mediated colistin resistance gene among Gram-negative bacilli in the hospital. This possibly highlights the frequent misuse of colistin in animal husbandry from this rural area. The findings underscore the importance of monitoring resistance patterns and implementing stringent infection control measures.},
}

@article {pmid39801834,
year = {2025},
author = {Bustamante, M and Mei, S and Daras, IM and van Doorn, GS and Falcao Salles, J and de Vos, MGJ},
title = {An eco-evolutionary perspective on antimicrobial resistance in the context of One Health.},
journal = {iScience},
volume = {28},
number = {1},
pages = {111534},
pmid = {39801834},
issn = {2589-0042},
abstract = {The One Health approach musters growing concerns about antimicrobial resistance due to the increased use of antibiotics in healthcare and agriculture, with all of its consequences for human, livestock, and environmental health. In this perspective, we explore the current knowledge on how interactions at different levels of biological organization, from genetic to ecological interactions, affect the evolution of antimicrobial resistance. We discuss their role in different contexts, from natural systems with weak selection, to human-influenced environments that impose a strong pressure toward antimicrobial resistance evolution. We emphasize the need for an eco-evolutionary approach within the One Health framework and highlight the importance of horizontal gene transfer and microbiome interactions for increased understanding of the emergence and spread of antimicrobial resistance.},
}

@article {pmid39786570,
year = {2025},
author = {Chen, J and Garfinkel, DJ and Bergman, CM},
title = {Horizontal Transfer and Recombination Fuel Ty4 Retrotransposon Evolution in Saccharomyces.},
journal = {Genome biology and evolution},
volume = {17},
number = {1},
pages = {},
doi = {10.1093/gbe/evaf004},
pmid = {39786570},
issn = {1759-6653},
support = {//University of Georgia Research Foundation/ ; R01GM124216/NH/NIH HHS/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Retroelements ; *Saccharomyces/genetics ; *Evolution, Molecular ; *Recombination, Genetic ; Phylogeny ; Genome, Fungal ; },
abstract = {Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes; however, the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genus Saccharomyces using short- and long-read whole genome sequence data, including new PacBio genome assemblies for two Saccharomyces mikatae strains. We find evidence for multiple independent HTT events introducing the Tsu4 subfamily into specific lineages of Saccharomyces paradoxus, Saccharomyces cerevisiae, Saccharomyces eubayanus, Saccharomyces kudriavzevii and the ancestor of the S. mikatae/Saccharomyces jurei species pair. In both S. mikatae and S. kudriavzevii, we identified novel Ty4 clades that were independently generated through recombination between resident and horizontally transferred subfamilies. Our results reveal that recurrent HTT and lineage-specific extinction events lead to a complex pattern of Ty4 subfamily content across the genus Saccharomyces. Moreover, our results demonstrate how HTT can lead to coexistence of related retrotransposon subfamilies in the same genome that can fuel evolution of new retrotransposon clades via recombination.},
}

*Gene Transfer, Horizontal
*Retroelements
*Saccharomyces/genetics
*Evolution, Molecular
*Recombination, Genetic
Phylogeny
Genome, Fungal

@article {pmid39750749,
year = {2025},
author = {Molari, M and Shaw, LP and Neher, RA},
title = {Quantifying the Evolutionary Dynamics of Structure and Content in Closely Related E. coli Genomes.},
journal = {Molecular biology and evolution},
volume = {42},
number = {1},
pages = {},
doi = {10.1093/molbev/msae272},
pmid = {39750749},
issn = {1537-1719},
support = {//University of Basel/ ; //Sir Henry Wellcome Postdoctoral Fellow/ ; 220422/Z/20/Z//Wellcome/ ; },
mesh = {*Escherichia coli/genetics ; *Genome, Bacterial ; *Evolution, Molecular ; *Phylogeny ; Synteny ; },
abstract = {Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics of accessory genome evolution are very poorly understood, in contrast to the core genome where diversification is readily described by mutations and homologous recombination. Here, we tackle this problem for the case of very closely related genomes. We comprehensively describe genome evolution within n=222 genomes of Escherichia coli ST131, which likely shared a common ancestor around 100 years ago. After removing putative recombinant diversity, the total length of the phylogeny is 6,000 core genome substitutions. Within this diversity, we find 22 modifications to core genome synteny and estimate around 2,000 structural changes within the accessory genome, i.e. one structural change for every three core genome substitutions. Sixty-three percent of loci with structural diversity could be resolved into individual gain and loss events with 10-fold more gains than losses, demonstrating a dominance of gains due to insertion sequences and prophage integration. Our results suggest the majority of synteny changes and insertions in our dataset are likely deleterious and only persist for a short time before being removed by purifying selection.},
}

*Escherichia coli/genetics
*Genome, Bacterial
*Evolution, Molecular
*Phylogeny
Synteny

@article {pmid39693608,
year = {2024},
author = {Laidlaw, A and Blondin-Brosseau, M and Shay, J and Dussault, F and Rao, M and Petronella, N and Tamber, S},
title = {Variation in plasmid conjugation among nontyphoidal Salmonella enterica serovars.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2024-0164},
pmid = {39693608},
issn = {1480-3275},
abstract = {Conjugation is a complex phenomenon involving multiple plasmid, bacterial, and environmental factors. Here we describe an IncI1 plasmid encoding multidrug antibiotic resistance to aminoglycosides, sulfonamides, and third-generation cephalosporins. This plasmid is widespread geographically among animal, human, and environmental sectors. We present data on the transmissibility of this plasmid from Salmonella enterica ser. Kentucky into 40 strains of S. enterica (10 strains each from serovars Enteritidis, Heidelberg, Infantis, and Typhimurium). Thirty seven out of 40 strains were able to take up the plasmid. Rates of conjugation were variable between strains ranging from 10[-8] to 10[-4]. Overall, serovars Enteritidis and Typhimurium demonstrated the highest rates of conjugation, followed by Heidelberg, and then Infantis. No relationships were observed between the recipient cell surface and rate of conjugation. Recipient cell numbers correlated positively with conjugation rate and strains with high conjugation rates had marginally but significantly higher growth parameters compared to strains that took up the plasmid at lower frequencies. Environmental conditions known to impact cell growth, such as temperature, nutrient availability, and the presence of antibiotics, had a modulating effect on conjugation. Collectively, these results will further understanding of plasmid transmission dynamics in Salmonella, which is a critical first step towards the development of mitigation strategies.},
}

@article {pmid39801293,
year = {2025},
author = {Marquiegui-Alvaro, A and Kottara, A and Chacón, M and Cliffe, L and Brockhurst, M and Dixon, N},
title = {Genetic Bioaugmentation-Mediated Bioremediation of Terephthalate in Soil Microcosms Using an Engineered Environmental Plasmid.},
journal = {Microbial biotechnology},
volume = {18},
number = {1},
pages = {e70071},
pmid = {39801293},
issn = {1751-7915},
support = {BB/P01738X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T005742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/W012723/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/S022856/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {*Plasmids/genetics ; *Soil Microbiology ; *Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Phthalic Acids/metabolism ; Gene Transfer, Horizontal ; Pseudomonas putida/genetics/metabolism ; },
abstract = {Harnessing in situ microbial communities to clean-up polluted natural environments is a potentially efficient means of bioremediation, but often the necessary genes to breakdown pollutants are missing. Genetic bioaugmentation, whereby the required genes are delivered to resident bacteria via horizontal gene transfer, offers a promising solution to this problem. Here, we engineered a conjugative plasmid previously isolated from soil, pQBR57, to carry a synthetic set of genes allowing bacteria to consume terephthalate, a chemical component of plastics commonly released during their manufacture and breakdown. Our engineered plasmid caused a low fitness cost and was stably maintained in terephthalate-contaminated soil by the bacterium P. putida. Plasmid carriers efficiently bioremediated contaminated soil in model soil microcosms, achieving complete breakdown of 3.2 mg/g of terephthalate within 8 days. The engineered plasmid horizontally transferred the synthetic operon to P. fluorescens in situ, and the resulting transconjugants degraded 10 mM terephthalate during a 180-h incubation. Our findings show that environmental plasmids carrying synthetic catabolic operons can be useful tools for in situ engineering of microbial communities to perform clean-up even of complex environments like soil.},
}

*Plasmids/genetics
*Soil Microbiology
*Biodegradation, Environmental
*Soil Pollutants/metabolism
*Phthalic Acids/metabolism
Gene Transfer, Horizontal
Pseudomonas putida/genetics/metabolism

@article {pmid39799674,
year = {2025},
author = {Li, Y and Qin, W and Xin, X and Tang, C and Huang, Y and He, X and Chen, L and Yu, G and Yu, F},
title = {Dynamic impact of polyethylene terephthalate nanoplastics on antibiotic resistance and microplastics degradation genes in the rhizosphere of Oryza sativa L.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137173},
doi = {10.1016/j.jhazmat.2025.137173},
pmid = {39799674},
issn = {1873-3336},
abstract = {This study examined the effects of polyethylene terephthalate (PET) nanoplastics on the rhizosphere of Oryza sativa L., focusing on dynamic changes and interactions among microbial communities, antibiotic resistance genes (ARGs) and microplastic degradation genes (MDGs). PET exposure altered the structure and function of soil microbial, enabling specific microbial groups to thrive in polluted environments. High-dose PET treatments markedly increased the abundance and dissemination of ARGs, primarily via resistance mechanisms such as antibiotic efflux and target alteration. By providing additional carbon sources and surfaces for microbial attachment, PET stimulated the growth of microorganisms harboring MDGs, resulting in an increase in MDGs abundance. The elevated expression of MDGs facilitated the propagation of ARGs, with overlapping host microorganisms suggesting that certain microbial groups exhibit dual metabolic capabilities, enabling them to endure both antibiotic and microplastic pressures. Toxic byproducts of microplastic degradation, such as mono-ethylhexyl phthalate, further promoted ARGs dissemination by increasing horizontal gene transfer frequency. Structural equation modeling revealed that PET indirectly influenced ARGs and MDGs expression by altering soil C/N ratio, available phosphorus, and enzyme activities. Thus, nanoscale PET exacerbates ecological risks to soil microbial communities by driving co-propagation of ARGs and MDGs, highlighting the persistent threat of composite pollution to agroecosystems.},
}

@article {pmid39798650,
year = {2025},
author = {Zhang, X and Guo, W and Zhang, Z and Gao, P and Tang, P and Liu, T and Yao, X and Li, J},
title = {Insights into the mobility and bacterial hosts of antibiotic resistance genes under dinotefuran selection pressure in aerobic granular sludge based on metagenomic binning and functional modules.},
journal = {Environmental research},
volume = {268},
number = {},
pages = {120807},
doi = {10.1016/j.envres.2025.120807},
pmid = {39798650},
issn = {1096-0953},
abstract = {Dinotefuran (DIN) is toxic to non-target organisms and accelerates the evolution of antibiotic resistance, which poses a problem for the stable operation of the activated sludge process in wastewater treatment plants (WWTPs). However, the emergence and the transfer mechanism of antibiotic resistance genes (ARGs) in activated sludge systems under DIN stress remains unclear. Thus, in the study, the potential impact of DIN on ARGs and virulence factor genes (VFGs) in aerobic granular sludge (AGS) was investigated in depth using metagenomic binning and functional modules. It was found that DIN stress increased the total abundance of ARGs, mobile genetic elements (MGEs), and VFGs in the AGS system, with the highest abundance of fabG (4.6%), tnpA (55.6%) and LPS (39.0%), respectively. The proliferation of the enteric pathogens Salmonella enterica and Escherichia coli in the system indicates that DIN induces exposure of harmless bacteria to the infected environment. The genera Nitrospira (1169 ARG subtypes) and Dechloromonas (663 ARG subtypes) were identified as the potentially antibiotic-resistant bacteria carrying the most ARGs and MGEs in the metagenome-assembled genomes. Co-localization patterns of some ARGs, MGEs, and the SOS response-related gene lexA were observed on metagenome-assembled contigs under high levels of DIN exposure, suggesting DIN stimulated ROS production (101.8% increase over control), altered cell membrane permeability, and increased the potential for horizontal gene transfer (HGT). Furthermore, the DNA damage caused by DIN in AGS led to the activation of the antioxidant system and the SOS repair response, which in turn promoted the expression of the type IV secretion system and HGT through the flagellar channel. This study extends the previously unappreciated DIN understanding of the spread and associated risks of ARGs and VFGs in the AGS system of WWTPs. It elucidates how DIN facilitates HGT, offering a scientific basis for controlling emerging contaminant-induced resistance.},
}

@article {pmid39575680,
year = {2025},
author = {Wang, H and Xu, Z and Zhang, Z and Zhong, B},
title = {Horizontal transposon transfer during plant terrestrialization.},
journal = {Journal of integrative plant biology},
volume = {67},
number = {1},
pages = {15-18},
doi = {10.1111/jipb.13809},
pmid = {39575680},
issn = {1744-7909},
support = {32122010//National Natural Science Foundation of China/ ; 32370228//National Natural Science Foundation of China/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Gene Transfer, Horizontal ; *Plants/genetics ; },
abstract = {During the move to land, plants acquired transposable elements by horizontal transfer from bacteria and fungi and land plants have many long non-coding RNAs derived from retrotransposons acquired by horizontal transposon transfer, including some that are highly expressed and involved in the response to drought stress and abscisic acid.},
}

*DNA Transposable Elements/genetics
*Gene Transfer, Horizontal
*Plants/genetics

@article {pmid39797530,
year = {2025},
author = {Liu, Y and Gong, C and Hu, Y and Han, H and Tian, T and Luo, Y and Yang, X and Xie, W and Wu, Q and Wang, S and Guo, Z and Zhang, Y},
title = {Silencing of the plant-derived horizontally transferred gene BtSC5DL effectively controls Bemisia tabaci MED.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8638},
pmid = {39797530},
issn = {1526-4998},
support = {2021YFD1400600//National Key R&D Program of China/ ; 32221004//National Natural Science Foundation of China/ ; CARS-23//Earmarked Fund for CARS/ ; Y2023XK15//Central Public-Interest Scientific Institution Basal Research Fund of the Chinese Academy of Agricultural Sciences./ ; Y2024XK01//Central Public-Interest Scientific Institution Basal Research Fund of the Chinese Academy of Agricultural Sciences./ ; //Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables/ ; CAAS-ASTIP-IVFCAAS//Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; },
abstract = {BACKGROUND: The whitefly Bemisia tabaci is a notorious agricultural pest known for its ability to cause significant crop damage through direct feeding and virus transmission. Its remarkable adaptability and reproductive capacity are linked to its ability to acquire and integrate horizontally transferred genes (HTGs) into its genome. These HTGs increase the physiological and metabolic capacities of this pest, including cholesterol synthesis, which is critical for its survival and reproductive success. Among these genes, we identified a plant-derived B. tabaci Δ7-sterol C5-desaturase-like gene (BtSC5DL), which plays a pivotal role in B. tabaci cholesterol metabolism and reproductive biology.

RESULTS: In this study, we cloned and identified the BtSC5DL gene from B. tabaci Mediterranean (MED). Bioinformatics and molecular analyses revealed that BtSC5DL was transferred from plants to B. tabaci millions of years ago and is now stably expressed in this species. Silencing BtSC5DL through dsRNA feeding resulted in significant reductions in egg production and cholesterol content in B. tabaci MED. Furthermore, virus-induced gene silencing (VIGS) experiments confirmed that long-term suppression of BtSC5DL had a notable ability to control whitefly populations.

CONCLUSION: Our results demonstrate the crucial role of BtSC5DL in cholesterol biosynthesis in B. tabaci MED and suggest that the acquisition of this gene significantly enhances the reproductive capacity of this species. These findings provide a theoretical basis for the development of RNA interference (RNAi)-based pest control strategies targeting BtSC5DL, offering a potential new approach for the effective management of whitefly populations in agricultural settings. © 2025 Society of Chemical Industry.},
}

@article {pmid39794121,
year = {2025},
author = {Liu, Y and Botelho, J and Iranzo, J},
title = {Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279300.124},
pmid = {39794121},
issn = {1549-5469},
abstract = {Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGE). However, because MGE are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short and long terms. By combining comparative genomics and phylogeny-aware statistical methods, we quantified the association between the presence of 7 widespread defense systems and the abundance of MGE in the genomes of 196 bacterial and 1 archaeal species. We also calculated the differences in the rates of gene gain and loss between lineages that possess and lack each defense system. Our results show that the impact of defense systems on HGT is highly taxon- and system-dependent, and in most cases not statistically significant. Timescale analysis reveals that defense systems must persist in a lineage for a relatively long time to exert an appreciable negative impact on HGT. In contrast, for shorter evolutionary timescales, frequent co-acquisition of MGE and defense systems results in a net positive association of the latter with HGT. Given the high turnover rates experienced by defense systems, we propose that the inhibitory effect of most defense systems on HGT is masked by their strong linkage with MGE. These findings help explain the contradictory conclusions of previous research by pointing at mobility and within-host retention times as key factors that determine the impact of defense systems on genome plasticity.},
}

@article {pmid39793087,
year = {2025},
author = {Zhang, Y and Tu, C and Bai, J and Li, X and Sun, Z and Xu, L},
title = {Metabolic enhancement contributed by horizontal gene transfer is essential for dietary specialization in leaf beetles.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {1},
pages = {e2415717122},
doi = {10.1073/pnas.2415717122},
pmid = {39793087},
issn = {1091-6490},
support = {32370523//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Coleoptera/genetics/metabolism ; *Gene Transfer, Horizontal ; *Plant Leaves/parasitology/metabolism/genetics ; *Larva/metabolism/genetics/growth & development ; *Cellulose/metabolism ; Diet ; },
abstract = {Horizontal gene transfer (HGT) from bacteria to insects is widely reported and often associated with the adaptation and diversification of insects. However, compelling evidence demonstrating how HGT-conferred metabolic adjustments enable species to adapt to surrounding environment remains scarce. Dietary specialization is an important ecological strategy adopted by animals to reduce inter- and intraspecific competition for limited resources. Adults of the leaf beetle Plagiodera versicolora (Coleoptera) preferentially consume new leaves; nevertheless, we found that they selectively oviposit on mature leaves, thereby establishing a distinct dietary niche separation between adults and larvae. Based on the de novo assembled chromosome-level genome, we identified two horizontally transferred genes with cellulose degradation potential, belonging to the glycosyl hydrolase 48 family (GH48-1 and GH48-2). Prokaryotic expression of the HGTs confirmed the cellulose degradation capability of the two genes. Knockdown of GH48 significantly hampered the growth and survival rate of larvae feeding on mature leaves compared to wild-type larvae, with no similar effect observed in adults. Replenishing the GH48-expressing bacteria compensated for the knockdown of these two genes and recurred larval adaptability to mature leaves. Taken together, our results highlight the advantage and metabolic enhancement conferred by the two cellulose-degrading HGTs in P. versicolora larvae, enabling their development on cellulose-enriched mature leaves and underscoring the indispensable role of HGTs in facilitating the adaptation of leaf beetles to plants.},
}

Animals
*Coleoptera/genetics/metabolism
*Gene Transfer, Horizontal
*Plant Leaves/parasitology/metabolism/genetics
*Larva/metabolism/genetics/growth & development
*Cellulose/metabolism
Diet

@article {pmid39791879,
year = {2025},
author = {Kohlmeier, MG and O'Hara, GW and Ramsay, JP and Terpolilli, JJ},
title = {Closed genomes of commercial inoculant rhizobia provide a blueprint for management of legume inoculation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0221324},
doi = {10.1128/aem.02213-24},
pmid = {39791879},
issn = {1098-5336},
abstract = {UNLABELLED: Rhizobia are soil bacteria capable of establishing symbiosis within legume root nodules, where they reduce atmospheric N2 into ammonia and supply it to the plant for growth. Australian soils often lack rhizobia compatible with introduced agricultural legumes, so inoculation with exotic strains has become a common practice for over 50 years. While extensive research has assessed the N2-fixing capabilities of these inoculants, their genomics, taxonomy, and core and accessory gene phylogeny are poorly characterized. Furthermore, in some cases, inoculant strains have been developed from isolations made in Australia. It is unknown whether these strains represent naturalized exotic organisms, native rhizobia with a capacity to nodulate introduced legumes, or recombinant strains arising from horizontal transfer between introduced and native bacteria. Here, we describe the complete, closed genome sequences of 42 Australian commercial rhizobia. These strains span the genera, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium, and Sinorhizobium, and only 23 strains were identified to species level. Within inoculant strain genomes, replicon structure and location of symbiosis genes were consistent with those of model strains for each genus, except for Rhizobium sp. SRDI969, where the symbiosis genes are chromosomally encoded. Genomic analysis of the strains isolated from Australia showed they were related to exotic strains, suggesting that they may have colonized Australian soils following undocumented introductions. These genome sequences provide the basis for accurate strain identification to manage inoculation and identify the prevalence and impact of horizontal gene transfer (HGT) on legume productivity.

IMPORTANCE: Inoculation of cultivated legumes with exotic rhizobia is integral to Australian agriculture in soils lacking compatible rhizobia. The Australian inoculant program supplies phenotypically characterized high-performing strains for farmers but in most cases, little is known about the genomes of these rhizobia. Horizontal gene transfer (HGT) of symbiosis genes from inoculant strains to native non-symbiotic rhizobia frequently occurs in Australian soils and can impact the long-term stability and efficacy of legume inoculation. Here, we present the analysis of reference-quality genomes for 42 Australian commercial rhizobial inoculants. We verify and classify the genetics, genome architecture, and taxonomy of these organisms. Importantly, these genome sequences will facilitate the accurate strain identification and monitoring of inoculants in soils and plant nodules, as well as enable detection of horizontal gene transfer to native rhizobia, thus ensuring the efficacy and integrity of Australia's legume inoculation program.},
}

@article {pmid39789078,
year = {2025},
author = {Lee, D and Muir, P and Lundberg, S and Lundholm, A and Sandegren, L and Koskiniemi, S},
title = {A CRISPR-Cas9 system protecting E. coli against acquisition of antibiotic resistance genes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1545},
pmid = {39789078},
issn = {2045-2322},
mesh = {*CRISPR-Cas Systems ; *Escherichia coli/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; },
abstract = {Antimicrobial resistance (AMR) is an increasing problem worldwide, and new treatment options for bacterial infections are direly needed. Engineered probiotics show strong potential in treating or preventing bacterial infections. However, one concern with the use of live bacteria is the risk of the bacteria acquiring genes encoding for AMR or virulence factors through horizontal gene transfer (HGT), and the transformation of the probiotic into a superbug. Therefore, we developed an engineered CRISPR-Cas9 system that protects bacteria from horizontal gene transfer. We synthesized a CRISPR locus targeting eight AMR genes and cloned this with the Cas9 and transacting tracrRNA on a medium copy plasmid. We next evaluated the efficiency of the system to block HGT through transformation, transduction, and conjugation. Our results show that expression of the CRISPR-Cas9 system successfully protects E. coli MG1655 from acquiring the targeted resistance genes by transformation or transduction with 2-3 logs of protection depending on the system for transfer and the target gene. Furthermore, we show that the system blocks conjugation of a set of clinical plasmids, and that the system is also able to protect the probiotic bacterium E. coli Nissle 1917 from acquiring AMR genes.},
}

*CRISPR-Cas Systems
*Escherichia coli/genetics/drug effects
Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Plasmids/genetics
Anti-Bacterial Agents/pharmacology
Conjugation, Genetic

@article {pmid39623141,
year = {2025},
author = {Bhattacharya, S and Bejerano-Sagie, M and Ravins, M and Zeroni, L and Kaur, P and Gopu, V and Rosenshine, I and Ben-Yehuda, S},
title = {Flagellar rotation facilitates the transfer of a bacterial conjugative plasmid.},
journal = {The EMBO journal},
volume = {44},
number = {2},
pages = {587-611},
pmid = {39623141},
issn = {1460-2075},
support = {810186//EC | European Research Council (ERC)/ ; SPP2389//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {*Plasmids/genetics/metabolism ; *Flagella/genetics/metabolism ; *Conjugation, Genetic ; *Bacillus subtilis/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Promoter Regions, Genetic ; },
abstract = {Conjugation-mediated DNA delivery is the primary mode for antibiotic resistance spread in bacteria; yet, molecular mechanisms regulating the conjugation process remain largely unexplored. While conjugative plasmids typically require bacterial attachment to solid surfaces for facilitation of donor-to-recipient proximity, the pLS20 conjugative plasmid, prevalent among Gram-positive Bacillus spp., uniquely requires fluid environments to enhance its transfer. Here, we show that pLS20, carried by Bacillus subtilis, induces multicellular clustering, which can accommodate various species, hence offering a stable platform for DNA delivery in a liquid milieu. We further discovered that induction of pLS20 promoters, governing crucial conjugative genes, is dependent on the presence of donor cell flagella, the major bacterial motility organelle. Moreover, the pLS20 regulatory circuit is controlled by a mechanosensing signal transduction pathway responsive to flagella rotation, thus activating conjugation gene expression exclusively during the host motile phase. This flagella-conjugation coupling strategy may allow the dissemination of the plasmid to remote destinations, allowing infiltration into new niches.},
}

*Plasmids/genetics/metabolism
*Flagella/genetics/metabolism
*Conjugation, Genetic
*Bacillus subtilis/genetics/metabolism
Gene Expression Regulation, Bacterial
Bacterial Proteins/genetics/metabolism
Gene Transfer, Horizontal
Promoter Regions, Genetic

@article {pmid39788974,
year = {2025},
author = {Scarpa, A and Pianezza, R and Gellert, HR and Haider, A and Kim, BY and Lai, EC and Kofler, R and Signor, S},
title = {Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {516},
pmid = {39788974},
issn = {2041-1723},
support = {P35093//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P30 CA008748/CA/NCI NIH HHS/United States ; P34965//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; R01 HD108914/HD/NICHD NIH HHS/United States ; NSF-EPSCoR-2032756//National Science Foundation (NSF)/ ; R01 GM083300/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Retroelements/genetics ; *Gene Transfer, Horizontal ; *Phylogeny ; *Evolution, Molecular ; Drosophila/genetics ; Genome, Insect ; Drosophila melanogaster/genetics ; Introduced Species ; },
abstract = {Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. Here, we show that two retrotransposons, Shellder and Spoink, invaded the genomes of multiple species of the melanogaster subgroup within the last 50 years. Through horizontal transfer, Spoink spread in D. melanogaster during the 1980s, while both Shellder and Spoink invaded D. simulans in the 1990s. Possibly following hybridization, D. simulans infected the island endemic species D. mauritiana (Mauritius) and D. sechellia (Seychelles) with both TEs after 1995. In the same approximate time-frame, Shellder also invaded D. teissieri, a species confined to sub-Saharan Africa. We find that the donors of Shellder and Spoink are likely American Drosophila species from the willistoni, cardini, and repleta groups. Thus, the described cascade of TE invasions could only become feasible after D. melanogaster and D. simulans extended their distributions into the Americas 200 years ago, likely aided by human activity. Our work reveals that cascades of TE invasions, likely initiated by human-mediated range expansions, could have an impact on the genomic and phenotypic evolution of geographically dispersed species. Within a few decades, TEs could invade many species, including island endemics, with distributions very distant from the donor of the TE.},
}

Animals
*Retroelements/genetics
*Gene Transfer, Horizontal
*Phylogeny
*Evolution, Molecular
Drosophila/genetics
Genome, Insect
Drosophila melanogaster/genetics
Introduced Species

@article {pmid39788725,
year = {2025},
author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Wadsworth, CB},
title = {In vitro evolution of ciprofloxacin resistance in Neisseria commensals and derived mutation population dynamics in natural Neisseria populations.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae107},
pmid = {39788725},
issn = {1574-6968},
abstract = {Commensal Neisseria are members of a healthy human oropharyngeal microbiome; however, they also serve as a reservoir of antimicrobial resistance for their pathogenic relatives. Despite their known importance as sources of novel genetic variation for pathogens, we still do not understand the full suite of resistance mutations commensal species can harbor. Here, we use in vitro selection to assess the mutations that emerge in response to ciprofloxacin selection in commensal Neisseria by passaging 4 replicates of 4 different species in the presence of a selective antibiotic gradient for 20 days; then categorized derived mutations with whole genome sequencing. 10/16 selected cells lines across the 4 species evolved ciprofloxacin resistance (≥ 1 ug/ml); with resistance-contributing mutations primarily emerging in DNA gyrase subunit A and B (gyrA and gyrB), topoisomerase IV subunits C and E (parC and parE), and the multiple transferable efflux pump repressor (mtrR). Of note, these derived mutations appeared in the same loci responsible for ciprofloxacin reduced susceptibility in the pathogenic Neisseria, suggesting conserved mechanisms of resistance across the genus. Additionally, we tested for zoliflodacin cross-resistance in evolved strain lines and found 6 lineages with elevated zoliflodacin minimum inhibitory concentrations. Finally, to interrogate the likelihood of experimentally derived mutations emerging and contributing to resistance in natural Neisseria, we used a population-based approach and identified GyrA 91I as a substitution circulating within commensal Neisseria populations and ParC 85C in a single gonococcal isolate. A small cluster of gonococcal isolates shared commensal alleles at parE, suggesting recent cross-species recombination events.},
}

@article {pmid39787839,
year = {2025},
author = {Zhao, W and Hou, Y and Wei, L and Wei, W and Zhang, K and Duan, H and Ni, BJ},
title = {Chlorination-induced spread of antibiotic resistance genes in drinking water systems.},
journal = {Water research},
volume = {274},
number = {},
pages = {123092},
doi = {10.1016/j.watres.2025.123092},
pmid = {39787839},
issn = {1879-2448},
abstract = {Chlorine, the most widely utilized disinfectant for drinking water globally, has recently been implicated in facilitating the spread of antibiotic resistance genes (ARGs), raising concerns about its underestimated environmental and ecological risks. However, given the current fragmented research focus and results, a comprehensive understanding of the potential mechanisms and influencing factors behind chlorination-promoted ARGs transmission in drinking water systems is crucial. This work is the first to systematically review the variations in abundance, transmission mechanisms, influencing factors, and mitigation strategies related to ARGs during the chlorination process. The results indicated that chlorination could induce genetic mutations and promote horizontal gene transfer through multiple pathways, including increased reactive oxygen species, enhanced membrane permeability, stimulation of the SOS response, and activation of efflux pumps. In addition, this work delves into significant discoveries regarding the factors affecting ARG transmission in drinking water, such as chlorine concentration, reaction time, disinfection byproducts, pipe materials, biofilms, and the water matrix. A series of effective strategies from water source to point-of-use were proposed aimed at mitigating ARGs transmission risks in the drinking water system. Finally, we address existing challenges and outline future research directions to overcome these bottlenecks. Overall, this review aims to advance our understanding of the role of chlorination in the dissemination of ARGs and to inspire innovative research ideas for optimizing disinfection techniques, minimizing the risks of antibiotic resistance transmission, and enhancing the safety of drinking water.},
}

@article {pmid39780077,
year = {2025},
author = {Lv, C and Abdullah, M and Su, CL and Chen, W and Zhou, N and Cheng, Z and Chen, Y and Li, M and Simpson, KW and Elsaadi, A and Zhu, Y and Lipkin, SM and Chang, YF},
title = {Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {19},
pmid = {39780077},
issn = {1471-2164},
mesh = {Humans ; *Polyketide Synthases/genetics ; *Colitis, Ulcerative/microbiology/genetics ; *Escherichia coli/genetics/isolation & purification ; *Phylogeny ; *Genomic Islands ; Genome, Bacterial ; Genomics ; Gene Transfer, Horizontal ; Virulence Factors/genetics ; Escherichia coli Infections/microbiology ; Peptides ; Polyketides ; },
abstract = {The E. coli strains harboring the polyketide synthase (pks) island encode the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involves whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organisms. Fifteen E. coli strains isolated from patients with ulcerative colitis (UC) were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks-positive (pks[+]) isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158 + 13) pks[+] isolates belonged to phylogroup B2, and most of the isolates belong to sequence types ST73 and ST95. One isolate from a UC patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks[+] isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the0020preponderance of virulence genes and a reduced number of antimicrobial genes in pks[+] isolates. This study significantly contributes to understanding the evolution of pks islands in E. coli.},
}

Humans
*Polyketide Synthases/genetics
*Colitis, Ulcerative/microbiology/genetics
*Escherichia coli/genetics/isolation & purification
*Phylogeny
*Genomic Islands
Genome, Bacterial
Genomics
Gene Transfer, Horizontal
Virulence Factors/genetics
Escherichia coli Infections/microbiology
Peptides
Polyketides

@article {pmid39778056,
year = {2025},
author = {Silva, JK and Hervé, V and Mies, US and Platt, K and Brune, A},
title = {A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70010},
pmid = {39778056},
issn = {1462-2920},
support = {//Max-Planck-Gesellschaft/ ; },
mesh = {*Symbiosis ; Animals ; *Isoptera/microbiology ; *Genome, Bacterial ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Actinomycetales/genetics/metabolism ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/parasitology ; Metagenome ; },
abstract = {Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp. and other gut flagellates, representing the only known case of intracellular Actinomycetota in protists. Comparative analysis of eleven metagenome-assembled genomes from lower termites allowed us to describe them as new genera of Bifidobacteriaceae. Like the previously investigated Candidatus Ancillula trichonymphae, they ferment sugars via the bifidobacterium shunt but, unlike their free-living relatives, experienced significant genome erosion. Additionally, they acquired new functions by horizontal gene transfer from other gut bacteria, including the capacity to produce hydrogen. Members of the genus Ancillula (average genome size 1.56 ± 0.2 Mbp) retained most pathways for the synthesis of amino acids, including a threonine/serine exporter, providing concrete evidence for the basis of the mutualistic relationship with their host. By contrast, Opitulatrix species (1.23 ± 0.1 Mbp) lost most of their biosynthetic capacities, indicating that an originally mutualistic symbiosis is on the decline.},
}

*Symbiosis
Animals
*Isoptera/microbiology
*Genome, Bacterial
*RNA, Ribosomal, 16S/genetics
*Phylogeny
*Actinomycetales/genetics/metabolism
Gene Transfer, Horizontal
Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology/parasitology
Metagenome

@article {pmid39777960,
year = {2025},
author = {Perez, MF and Angelov, A and Übelacker, M and Torres Tejerizo, GA and Farias, ME and Liebl, W and Dib, JR},
title = {Linear Plasmids in Micrococcus: Insights Into a Common Ancestor and Transfer by Conjugation.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70020},
pmid = {39777960},
issn = {1462-2920},
support = {PICT 2018 N° 2545 PRESTAMO BID//Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación/ ; PIUNT A618/2//Universidad Nacional de Tucumán/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Micrococcus/genetics ; *Conjugation, Genetic ; Evolution, Molecular ; Phylogeny ; Open Reading Frames ; DNA, Bacterial/genetics ; Base Composition ; },
abstract = {Actinobacteria have frequently been reported in the Andean Puna, including strains of the genus Micrococcus. These strains demonstrate resistance to high levels of UV radiation, arsenic, and multiple antibiotics, and possess large linear plasmids. A comparative analysis of the sequences and putative functions of these plasmids was conducted. The presence of large regions with high sequence identity (exceeding 30 kb in total) in all three studied Micrococcus megaplasmids indicates a clear evolutionary link among these elements. Genes related to essential plasmid functions were primarily found within these conserved regions, while genes associated with resistance to metals and antibiotics resided in accessory regions. Moreover, the abundance of open reading frames related to transposition and recombination, along with local deviations from the average GC content, provides evidence for the mosaic nature and considerable genetic plasticity of these plasmids. This study presents evidence of a common ancestor for linear plasmids in Micrococcus and suggests that horizontal gene transfer likely occurs frequently within Andean lakes, providing the native microbial community with a beneficial gene pool to withstand extreme conditions. Additionally, the successful transfer of the linear plasmid pLMA1 by a DNase-insensitive, conjugation-type mechanism and its potential use as a genetic vector is demonstrated.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Micrococcus/genetics
*Conjugation, Genetic
Evolution, Molecular
Phylogeny
Open Reading Frames
DNA, Bacterial/genetics
Base Composition

@article {pmid39777461,
year = {2025},
author = {Blanchais, C and Pages, C and Campos, M and Boubekeur, K and Contarin, R and Orlando, M and Siguier, P and Laaberki, MH and Cornet, F and Charpentier, X and Rousseau, P},
title = {Interplay between the Xer recombination system and the dissemination of antibioresistance in Acinetobacter baumannii.},
journal = {Nucleic acids research},
volume = {53},
number = {1},
pages = {},
pmid = {39777461},
issn = {1362-4962},
support = {//University of Toulouse III Paul Sabatier/ ; ANR-AAPG2021-InXS//Agence Nationale de la Recherche/ ; ANR-11-LABX-0048//LabEx Ecofect/ ; ANR-11-IDEX-0007//Université de Lyon/ ; EQU202303016268//Fondation pour la Recherche Médicale/ ; ANR-AAPG2021-InXS//Agence Nationale de la Recherche/ ; },
mesh = {*Acinetobacter baumannii/genetics/drug effects ; *Plasmids/genetics ; *Recombination, Genetic ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Recombinases/metabolism/genetics ; Escherichia coli/genetics/drug effects ; },
abstract = {Antibiotic-resistant infections are a pressing clinical challenge. Plasmids are known to accelerate the emergence of resistance by facilitating horizontal gene transfer of antibiotic resistance genes between bacteria. We explore this question in Acinetobacter baumannii, a globally emerging nosocomial pathogen responsible for a wide range of infections with a worrying accumulation of resistance, particularly involving plasmids. In this species, plasmids of the Rep_3 family harbor antibiotic resistance genes within variable regions flanked by potential site-specific recombination sites recognized by the XerCD recombinase. We first show that the Xer system of A. baumannii functions as described in Escherichia coli, resolving chromosome dimers at the dif site and recombining plasmid-carried sites. However, the multiple Xer recombination sites found in Rep_3 plasmids do not allow excision of plasmid fragments. Rather, they recombine to cointegrate plasmids, which could then evolve to exchange genes. Cointegrates represent a significant fraction of the plasmid population and their formation is controlled by the sequence of recombination sites, which determines the compatibility between recombination sites. We conclude that plasmids in A. baumannii frequently recombine by Xer recombination, allowing a high level of yet controlled plasticity in the acquisition and combination of antibiotic resistance genes.},
}

*Acinetobacter baumannii/genetics/drug effects
*Plasmids/genetics
*Recombination, Genetic
Gene Transfer, Horizontal
Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Recombinases/metabolism/genetics
Escherichia coli/genetics/drug effects

@article {pmid39776180,
year = {2025},
author = {Shimuta, K and Ohama, Y and Ito, S and Hoshina, S and Takahashi, H and Igawa, G and Dorin Yamamoto, M and Akeda, Y and Ohnishi, M},
title = {Emergence of ceftriaxone-resistant Neisseria gonorrhoeae through horizontal gene transfer among Neisseria spp.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf008},
pmid = {39776180},
issn = {1537-6613},
abstract = {OBJECTIVES: It has been suggested that the emergence of ceftriaxone-resistant strains of Neisseria gonorrhoeae involves the incorporation of the penA gene from commensal Neisseria spp. that are resistant to ceftriaxone. However, the mechanism of this mosaic penA generation is unknown.

METHODS: We obtained 10 strains of commensal Neisseria spp. showing ceftriaxone MIC >0.5 mg/L. The similarity of the penA gene region of these commensal Neisseria spp. strains and some ceftriaxone-resistant N. gonorrhoeae strains was investigated. To obtain transformants, commensal Neisseria spp., Neisseria lactamica, gDNA was used as donor DNA and a N. gonorrhoeae strain as the recipient.

RESULTS: The sequence similarity in certain regions of penA-murE between some of the commensal Neisseria spp. strains and the N. gonorrhoeae FC428 strain was very high. The sequence of these regions was very similar among some ceftriaxone-resistant strains of Neisseria spp. The PenA of the transformants matched the full PenA 60 of the original FC428 strain. Furthermore, our findings indicated that the source of resistance could have been a penA fragment derived from Neisseria spp. that originally carried the same sequence.

CONCLUSIONS: We suggest that FC428 developed ceftriaxone resistance by acquiring part of the penA-murE gene region from N. lactamica through horizontal gene transfer. The ceftriaxone-resistant N. lactamica shown here may also have emerged by acquiring part of penA from other Neisseria spp. From this work, our data provide insights into the understanding of the mechanism underlying the evolution of drug-resistant gonorrhea-causing strains.},
}

@article {pmid39772912,
year = {2025},
author = {Figueroa, D and Ruiz, D and Tellini, N and De Chiara, M and Kessi-Pérez, EI and Martínez, C and Liti, G and Querol, A and Guillamón, JM and Salinas, F},
title = {Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0179424},
doi = {10.1128/spectrum.01794-24},
pmid = {39772912},
issn = {2165-0497},
abstract = {Nitrogen limitations in the grape must be the main cause of stuck fermentations during the winemaking process. In Saccharomyces cerevisiae, a genetic segment known as region A, which harbors 12 protein-coding genes, was acquired horizontally from a phylogenetically distant yeast species. This region is mainly present in the genome of wine yeast strains, carrying genes that have been associated with nitrogen utilization. Despite the putative importance of region A in yeast fermentation, its contribution to the fermentative process is largely unknown. In this work, we used a wine yeast strain to evaluate the contribution of region A to the fermentation process. To do this, we first sequenced the genome of the wine yeast strain using long-read sequencing and determined that region A is present in a single copy. We then implemented an optogenetic system in this wine yeast strain to precisely regulate the expression of each gene, generating a collection of 12 strains that allow for light-activated gene expression. To evaluate the role of these genes during fermentation, we assayed this collection using microculture and fermentation experiments in synthetic must with varying amounts of nitrogen concentration. Our results show that changes in gene expression for genes within this region can impact growth parameters and fermentation rate. We additionally found that the expression of various genes in region A is necessary to complete the fermentation process and prevent stuck fermentations under low nitrogen conditions. Altogether, our optogenetics-based approach demonstrates the importance of region A in completing fermentation under nitrogen-limited conditions.IMPORTANCEStuck fermentations due to limited nitrogen availability in grape must represent one of the main problems in the winemaking industry. Nitrogen limitation in grape must reduces yeast biomass and fermentation rate, resulting in incomplete fermentations with high levels of residual sugar, undesired by-products, and microbiological instability. Here, we used an optogenetic approach to demonstrate that expression of genes within region A is necessary to complete fermentations under low nitrogen availability. Overall, our results suggest that region A is a genetic signature for adaptation to low nitrogen conditions.},
}

@article {pmid39771135,
year = {2024},
author = {Li, Z and Yuan, D},
title = {Metagenomic Analysis Reveals the Effects of Microplastics on Antibiotic Resistance Genes in Sludge Anaerobic Digestion.},
journal = {Toxics},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/toxics12120920},
pmid = {39771135},
issn = {2305-6304},
support = {No. 52170097//the National Natural Science Foundation of China/ ; },
abstract = {Sewage sludge is recognized as both a source and a reservoir for antibiotic resistance genes (ARGs). Within an anaerobic digestion (AD) system, the presence of microplastics (MPs) has been observed to potentially facilitate the proliferation of these ARGs. Understanding the influence of MPs on microbial behavior and horizontal gene transfer (HGT) within the AD system is crucial for effectively managing the dissemination of ARGs in the environment. This study utilized metagenomic approaches to analyze the dynamics of various types of ARGs and potential microbial mechanisms under exposure to MPs during the AD process. The findings indicated that MPs in the AD process can enhance the proliferation of ARGs, with the extent of this enhancement increasing with the dosage of MPs: polyethylene (PE), polyethylene terephthalate (PET), and polylactic acid (PLA) MPs increased the abundance of ARGs in the anaerobic digestion system by up to 29.90%, 18.64%, and 14.15%, respectively. Additionally, the presence of MPs increased the relative abundance of mobile genetic elements (MGEs) during the AD process. Network correlation analysis further revealed that plasmids represent the predominant category of MGEs involved in the HGT of ARGs. Propionibacterium and Alicycliphilus were identified as the primary potential hosts for these ARGs. The results of gene function annotation indicated that exposure to MPs led to an increased the relative abundance of genes related to the production of reactive oxygen species (ROS), alterations in membrane permeability, ATP synthesis, and the secretion of extracellular polymeric substances (EPS). These genes play crucial roles in influencing the HGT of ARGs.},
}

@article {pmid39566460,
year = {2025},
author = {Xia, L and Wang, J and Chen, M and Li, G and Wang, W and An, T},
title = {Biofilm formation mechanisms of mixed antibiotic-resistant bacteria in water: Bacterial interactions and horizontal transfer of antibiotic-resistant plasmids.},
journal = {Journal of hazardous materials},
volume = {481},
number = {},
pages = {136554},
doi = {10.1016/j.jhazmat.2024.136554},
pmid = {39566460},
issn = {1873-3336},
mesh = {*Biofilms/drug effects/growth & development ; *Plasmids/genetics ; *Gene Transfer, Horizontal ; *Escherichia coli/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Water Microbiology ; Bacteria/drug effects/genetics/metabolism ; Microbial Interactions ; },
abstract = {Over 95 % of bacteria on water supply pipeline surfaces exist in biofilms, which are hotspots for antibiotic resistance gene (ARG) transmission. This study established mixed biofilm culture systems on a metal iron substrate using Escherichia coli: antibiotic-sensitive bacteria (ASB) and antibiotic-resistant bacteria (ARB). The growth rate and extracellular polymeric substances (EPS) content of mixed biofilm surpassed single-species biofilms due to synergistic interactions among different bacteria. However, the composition of mixed biofilms formed by ASB and ARB became unstable after 72 h, linked to reduced polysaccharide proportions in EPS and inter-bacterial competition. The bacterial composition and conjugative transfer frequency of ARGs in mixed biofilms indicate that biofilm formation significantly enhances horizontal transfer of ARGs. Notably, the conjugative transfer frequency of the mixed biofilm formed by two ARB increased 100-fold within five days. In contrast, the conjugative transfer frequency in the mixed biofilm formed by ASB and ARB was unstable; inter-bacterial competition led to plasmid loss associated with horizontal transfer of ARGs, ultimately resulting in biofilm shedding. Furthermore, genes associated with ARG transfer and biofilm growth up-regulated by 1.5 - 6 and 2 - 7 times, respectively, in mixed biofilm. These findings highlight a mutually reinforcing relationship between biofilm formation and horizontal ARG transmission, with significant environmental implications.},
}

*Biofilms/drug effects/growth & development
*Plasmids/genetics
*Gene Transfer, Horizontal
*Escherichia coli/drug effects/genetics
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Water Microbiology
Bacteria/drug effects/genetics/metabolism
Microbial Interactions

@article {pmid39770765,
year = {2024},
author = {Cangioli, L and Tabacchioni, S and Visca, A and Fiore, A and Aprea, G and Ambrosino, P and Ercole, E and Sørensen, S and Mengoni, A and Bevivino, A},
title = {Genome Insights into Beneficial Microbial Strains Composing SIMBA Microbial Consortia Applied as Biofertilizers for Maize, Wheat and Tomato.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122562},
pmid = {39770765},
issn = {2076-2607},
support = {862695//European Union's Horizon 2020/ ; },
abstract = {For the safe use of microbiome-based solutions in agriculture, the genome sequencing of strains composing the inoculum is mandatory to avoid the spread of virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Moreover, the annotated genomes can enable the design of specific primers to trace the inoculum into the soil and provide insights into the molecular and genetic mechanisms of plant growth promotion and biocontrol activity. In the present work, the genome sequences of some members of beneficial microbial consortia that have previously been tested in greenhouse and field trials as promising biofertilizers for maize, tomato and wheat crops have been determined. Strains belong to well-known plant-growth-promoting bacterial genera such as Bacillus, Burkholderia, Pseudomonas and Rahnella. The genome size of strains ranged from 4.5 to 7.5 Mbp, carrying many genes spanning from 4402 to 6697, and a GC content of 0.04% to 3.3%. The annotation of the genomes revealed the presence of genes that are implicated in functions related to antagonism, pathogenesis and other secondary metabolites possibly involved in plant growth promotion and gene clusters for protection against oxidative damage, confirming the plant-growth-promoting (PGP) activity of selected strains. All the target genomes were found to possess at least 3000 different PGP traits, belonging to the categories of nitrogen acquisition, colonization for plant-derived substrate usage, quorum sensing response for biofilm formation and, to a lesser extent, bacterial fitness and root colonization. No genes putatively involved in pathogenesis were identified. Overall, our study suggests the safe application of selected strains as "plant probiotics" for sustainable agriculture.},
}

@article {pmid39770663,
year = {2024},
author = {Ben Natan, M and Masasa, M and Shashar, N and Guttman, L},
title = {Antibiotic Resistance in Vibrio Bacteria Associated with Red Spotting Disease in Sea Urchin Tripneustes gratilla (Echinodermata).},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122460},
pmid = {39770663},
issn = {2076-2607},
support = {3-0000-17701//The Israeli Ministry of Health/ ; },
abstract = {The red spotting disease harms sea urchins to the extent of mass mortality in the ocean and echinocultures, accompanied by environmental damage and economic losses. The current study emphasizes the antimicrobial resistance of three isolated bacteria, closely related to Vibrio harveyi, Vibrio owensii, and Vibrio fortis, associated with red spotting in the cultured sea urchin Tripneustes gratilla. In vitro trials examined the susceptibility of these bacterial isolates to various antibiotics. In addition, using an in silico examination, we revealed the arsenal of antimicrobial resistance genes in available genomes of various pathogenic Vibrio associated with diseases in sea urchins, fish, shellfish, and corals. These two approaches enabled the discussion of the similarities and differences between aquatic pathogenic Vibrio and their antibiotic resistance. Among them, we revealed a core resistance to tetracyclines and penams by the in vitro examined strains. At the same time, the in silico study also supported this core resistance by the presence of the adeF and CRP genes in the bacterial genomes. Nevertheless, variability and specific resistance were evident at the species and strain levels in the Vibrio bacteria and genomes. The in vitro trials highlighted the diverse resistance of the Vibrio harveyi-like isolate to all examined antibiotics, while the other two isolates were found susceptible to nitrofurantoin and sulfamethoxazole. The resistance of the Vibrio harveyi-like isolate could not have been obtained in the genome of the proposed relative of Vibrio harveyi VHJR7 that lacks the oqxA and oqxB genes, which enables such a resistance. A unique sensitivity of the Vibrio fortis-like isolate to erythromycin is proposed when compared to other isolated Vibrio and Vibrio genomes that seem capable of resisting this drug. According to the results, we propose nitrofurantoin or sulfamethoxazole for treating two of the red-spotting-associated isolates (Vibrio fortis and Vibrio owensii-like), but not Vibrio harveyi-like. We assume that a shared resistance to some antibiotics by Vibrios is gained by a horizontal gene transfer while previous exposures of a bacterial strain to a specific drug may induce the development of a unique resistance. Finally, we discuss the novel knowledge on antibiotic resistance in Vibrio from the current research in light of the potential risks when using drugs for disease control in aquaculture.},
}

@article {pmid39770308,
year = {2024},
author = {Islam, MM and Jung, DE and Shin, WS and Oh, MH},
title = {Colistin Resistance Mechanism and Management Strategies of Colistin-Resistant Acinetobacter baumannii Infections.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/pathogens13121049},
pmid = {39770308},
issn = {2076-0817},
support = {Grant Nos. 2022R1F1A1071415 and NRF-RS-2023-00275307 and Grant No. 2019R1A6C1010033//National Research Foundation of Korea (NRF) funded by the Ministry of Education & Basic Science Research Capacity Enhancement Project through Korea Basic Science Institute (National research Facilities and Equipment Center) grant funded by the Ministry o/ ; },
mesh = {*Acinetobacter baumannii/drug effects/genetics ; *Colistin/pharmacology/therapeutic use ; Humans ; *Acinetobacter Infections/drug therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Drug Resistance, Bacterial/genetics/drug effects ; Animals ; },
abstract = {The emergence of antibiotic-resistant Acinetobacter baumannii (A. baumannii) is a pressing threat in clinical settings. Colistin is currently a widely used treatment for multidrug-resistant A. baumannii, serving as the last line of defense. However, reports of colistin-resistant strains of A. baumannii have emerged, underscoring the urgent need to develop alternative medications to combat these serious pathogens. To resist colistin, A. baumannii has developed several mechanisms. These include the loss of outer membrane lipopolysaccharides (LPSs) due to mutation of LPS biosynthetic genes, modification of lipid A (a constituent of LPSs) structure through the addition of phosphoethanolamine (PEtN) moieties to the lipid A component by overexpression of chromosomal pmrCAB operon genes and eptA gene, or acquisition of plasmid-encoded mcr genes through horizontal gene transfer. Other resistance mechanisms involve alterations of outer membrane permeability through porins, the expulsion of colistin by efflux pumps, and heteroresistance. In response to the rising threat of colistin-resistant A. baumannii, researchers have developed various treatment strategies, including antibiotic combination therapy, adjuvants to potentiate antibiotic activity, repurposing existing drugs, antimicrobial peptides, nanotechnology, photodynamic therapy, CRISPR/Cas, and phage therapy. While many of these strategies have shown promise in vitro and in vivo, further clinical trials are necessary to ensure their efficacy and widen their clinical applications. Ongoing research is essential for identifying the most effective therapeutic strategies to manage colistin-resistant A. baumannii. This review explores the genetic mechanisms underlying colistin resistance and assesses potential treatment options for this challenging pathogen.},
}

*Acinetobacter baumannii/drug effects/genetics
*Colistin/pharmacology/therapeutic use
Humans
*Acinetobacter Infections/drug therapy
*Anti-Bacterial Agents/therapeutic use/pharmacology
Drug Resistance, Multiple, Bacterial/genetics/drug effects
Drug Resistance, Bacterial/genetics/drug effects
Animals

@article {pmid39766551,
year = {2024},
author = {Li, R and Dai, H and Wang, W and Peng, R and Yu, S and Zhang, X and Huo, ZY and Yuan, Q and Luo, Y},
title = {Local Electric Field-Incorporated In-Situ Copper Ions Eliminating Pathogens and Antibiotic Resistance Genes in Drinking Water.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/antibiotics13121161},
pmid = {39766551},
issn = {2079-6382},
support = {2022YFC3205400//National Key R&D Program of China/ ; 42377436 & 52200079//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND/OBJECTIVES: Pathogen inactivation and harmful gene destruction from water just before drinking is the last line of defense to protect people from waterborne diseases. However, commonly used disinfection methods, such as chlorination, ultraviolet irradiation, and membrane filtration, experience several challenges such as continuous chemical dosing, the spread of antibiotic resistance genes (ARGs), and intensive energy consumption.

METHODS: Here, we perform a simultaneous elimination of pathogens and ARGs in drinking water using local electric fields and in-situ generated trace copper ions (LEF-Cu) without external chemical dosing. A 100-μm thin copper wire placed in the center of a household water pipe can generate local electric fields and trace copper ions near its surface after an external low voltage is applied.

RESULTS: The local electric field rapidly damages the outer structure of microorganisms through electroporation, and the trace copper ions can effectively permeate the electroporated microorganisms, successfully damaging their nucleic acids. The LEF-Cu disinfection system achieved complete inactivation (>6 log removal) of Escherichia coli O157:H7, Pseudomonas aeruginosa PAO1, and bacteriophage MS2 in drinking water at 2 V for 2 min, with low energy consumption (10[-2] kWh/m[3]). Meanwhile, the system effectively damages both intracellular (0.54~0.64 log) and extracellular (0.5~1.09 log) ARGs and blocks horizontal gene transfer.

CONCLUSIONS: LEF-Cu disinfection holds promise for preventing horizontal gene transfer and providing safe drinking water for household applications.},
}

@article {pmid39766521,
year = {2024},
author = {de Andrade, FCC and Carvalho, MF and Figueiredo, AMS},
title = {Survival Strategies of Staphylococcus aureus: Adaptive Regulation of the Anti-Restriction Gene ardA-H1 Under Stress Conditions.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/antibiotics13121131},
pmid = {39766521},
issn = {2079-6382},
support = {443804/2018-4 and 307672/2019-0//Conselho Nacional de Desenvolvimento Científico e tecnológico (CNPq)/ ; E-26/210.875/2016, E-26/211.554/2019, E-26.200.952/2020, and E-26/203.941/2024//Fundação Carlos Chagas Filho de Amparo à Pesquisa (FAPERJ)/ ; 001//Fundação Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; INV-007641/GATES/Bill & Melinda Gates Foundation/United States ; },
abstract = {Background/Objective: The anti-restriction protein ArdA-H1, found in multiresistant Staphylococcus aureus (MRSA) strains from the ST239-SCCmecIII lineage, inhibits restriction-modification systems, fostering horizontal gene transfer (HGT) and supporting genetic adaptability and resistance. This study investigates the regulatory mechanisms controlling ardA-H1 expression in S. aureus under various stress conditions, including acidic pH, iron limitation, and vancomycin exposure, and explores the roles of the Agr quorum sensing system. Methods: The expression of ardA-H1 was analyzed in S. aureus strains exposed to environmental stressors using real-time quantitative reverse transcription PCR. Comparisons were made between Agr-functional and Agr-deficient strains. In addition, Agr inhibition was achieved using a heterologous Agr autoinducing peptide. Results: The Agr system upregulated ardA-H1 expression in acidic and iron-limited conditions. However, vancomycin induced ardA-H1 activation specifically in the Agr-deficient strain GV69, indicating that an alternative regulatory pathway controls ardA-H1 expression in the absence of agr. The vancomycin response in GV69 suggests that diminished quorum sensing may offer a survival advantage by promoting persistence and HGT-related adaptability. Conclusion: Overall, our findings provide new insights into the intricate relationships between quorum-sensing, stress responses, bacterial virulence, and genetic plasticity, enhancing our understanding of S. aureus adaptability in challenging environments.},
}

@article {pmid39765217,
year = {2025},
author = {Niault, T and van Houte, S and Westra, E and Swarts, DC},
title = {Evolution and ecology of anti-defence systems in phages and plasmids.},
journal = {Current biology : CB},
volume = {35},
number = {1},
pages = {R32-R44},
doi = {10.1016/j.cub.2024.11.033},
pmid = {39765217},
issn = {1879-0445},
mesh = {*Plasmids/genetics ; *Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; Archaea/genetics/virology ; Evolution, Molecular ; Biological Evolution ; Interspersed Repetitive Sequences ; },
abstract = {Prokaryotes (Bacteria and Archaea) encode a highly diversified arsenal of defence systems that protect them against mobile genetic elements, such as phages and plasmids. In turn, mobile genetic elements encode anti-defence systems that allow them to escape the activity of these defence systems. This has resulted in an evolutionary arms race in which defence systems and anti-defence systems evolve and adapt continuously, driving intriguing innovation and enormous diversification on both sides. Over 150 prokaryotic defence systems have been identified to date. Anti-defence systems are known for only a subset of these, but more are being discovered at a steady rate. Despite an increasing understanding of the highly diverse molecular mechanisms of anti-defence systems, their diverse evolutionary origins, the selective pressures they are subjected to, and their ecological importance and implications often remain obscure. In this review, we describe the diverse strategies that phage and plasmid anti-defence systems employ to escape host defence systems. We explore the evolutionary origins of anti-defence systems and describe different factors that exert selective pressure, affecting their maintenance and diversification. We describe how, in turn, defence systems themselves evolved to act upon anti-defence mechanisms, thereby adding a new layer to the co-evolutionary battle between prokaryotes and their mobile genetic elements. We discuss how the continuous selective pressures found in dynamic microbial communities promote the retention and diversification of these anti-defence systems. Finally, we consider the ecological implications for both hosts and their mobile genetic elements, noting how the balance of defence and anti-defence strategies can shape microbial community composition, influence horizontal gene transfer, and impact ecosystem stability.},
}

*Plasmids/genetics
*Bacteriophages/genetics/physiology
*Bacteria/virology/genetics
Archaea/genetics/virology
Evolution, Molecular
Biological Evolution
Interspersed Repetitive Sequences

@article {pmid39763003,
year = {2025},
author = {Feng, Y and Lu, X and Zhao, J and Li, H and Xu, J and Li, Z and Wang, M and Peng, Y and Tian, T and Yuan, G and Zhang, Y and Liu, J and Zhang, M and Zhu La, AT and Qu, G and Mu, Y and Guo, W and Wu, Y and Zhang, Y and Wang, D and Hu, Y and Kan, B},
title = {Regional antimicrobial resistance gene flow among the One Health sectors in China.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {3},
pmid = {39763003},
issn = {2049-2618},
support = {2022YFC2303900//National Key Research and Development Program of China/ ; 22193064//major projects of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; China ; *Gene Transfer, Horizontal ; *One Health ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; *Gene Flow ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Food Microbiology ; Metagenomics/methods ; Genes, Bacterial/genetics ; },
abstract = {BACKGROUND: Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance.

RESULTS: In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples. A total of 40 ARG types and 743 ARG subtypes were identified, with a predominance of multidrug resistance genes. Compared with microbes from human fecal samples, those from food and environmental samples showed a significantly higher load of ARGs. We revealed that dietary habits and occupational exposure significantly affect ARG abundance. Pseudomonadota, particularly Enterobacteriaceae, were identified as the main ARG carriers shaping the resistome. The resistome in food samples was found more affected by mobile genetic elements (MGEs), whereas in environmental samples, it was more associated with the microbial composition. We evidenced that horizontal gene transfer (HGT) mediated by plasmids and phages, together with strain transmission, particularly those associated with the Enterobacteriaceae members, drive regional ARG flow. Lifestyle, dietary habits, and occupational exposure are all correlated with ARG dissemination and flies and food are important potential sources of ARGs to humans. The widespread mobile carbapenemase gene, OXA-347, carried by non-Enterobacteriaceae bacteria in the human gut microbiota, requires particular attention. Finally, we showed that machine learning models based on microbiome profiles were effective in predicting the presence of carbapenem-resistant strains, suggesting a valuable approach for AMR surveillance.

CONCLUSIONS: Our study provides a full picture of regional ARG transmission among the One Health sectors in a county-level city in China, which facilitates a better understanding of the complex routes of ARG transmission and highlights new points of focus for AMR surveillance and control. Video Abstract.},
}

Humans
China
*Gene Transfer, Horizontal
*One Health
*Bacteria/genetics/classification/drug effects/isolation & purification
*Anti-Bacterial Agents/pharmacology
*Gene Flow
Feces/microbiology
Drug Resistance, Bacterial/genetics
Food Microbiology
Metagenomics/methods
Genes, Bacterial/genetics

@article {pmid39756571,
year = {2025},
author = {Heneghan, PG and Salzberg, LI and Wolfe, KH},
title = {Zymocin-like killer toxin gene clusters in the nuclear genomes of filamentous fungi.},
journal = {Fungal genetics and biology : FG & B},
volume = {},
number = {},
pages = {103957},
doi = {10.1016/j.fgb.2024.103957},
pmid = {39756571},
issn = {1096-0937},
abstract = {Zymocin-like killer toxins are anticodon nucleases secreted by some budding yeast species, which kill competitor yeasts by cleaving tRNA molecules. They are encoded by virus-like elements (VLEs), cytosolic linear DNA molecules that are also called killer plasmids. To date, toxins of this type have been found only in budding yeast species (Saccharomycotina). Here, we show that the nuclear genomes of many filamentous fungi (Pezizomycotina) contain small clusters of genes coding for a zymocin-like ribonuclease (γ-toxin), a chitinase (toxin α/β-subunit), and in some cases an immunity protein. The γ-toxins from Fusarium oxysporum and Colletotrichum siamense abolished growth when expressed intracellularly in S. cerevisiae. Phylogenetic analysis of glycoside hydrolase 18 (GH18) domains shows that the chitinase genes in the gene clusters are members of the previously described C-II subgroup of Pezizomycotina chitinases. We propose that the Pezizomycotina gene clusters originated by integration of a yeast-like VLE into the nuclear genome, but this event must have been ancient because (1) phylogenetically, the Pezizomycotina C-II chitinases and the Saccharomycotina VLE-encoded toxin α/β subunit chitinases are sister clades with neither of them nested inside the other, and (2) many of the Pezizomycotina toxin cluster genes contain introns, whereas VLEs do not. One of the toxin gene clusters in Fusarium graminearum is a locus that has previously been shown to be under diversifying selection in North American populations of this plant pathogen. We also show that two genera of agaric mushrooms (Basidiomycota) have acquired toxin gene clusters by horizontal transfers from different Pezizomycotina donors.},
}

@article {pmid39754881,
year = {2025},
author = {Li, X and Zhang, Z and Liu, H and Wen, H and Wang, Q},
title = {The fate of intracellular and extracellular antibiotic resistance genes during ultrafiltration-ultraviolet-chlorination in a full-scale wastewater tretament plant.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {137088},
doi = {10.1016/j.jhazmat.2024.137088},
pmid = {39754881},
issn = {1873-3336},
abstract = {Effluent from wastewater treatment plants (WWTPs) is recognized as a significant source of antibiotic resistance genes (ARGs) in the environment. Advanced treatment processes such as ultrafiltration (UF), ultraviolet (UV) light disinfection, and chlorination have emerged as promising approaches for ARG removal. However, the efficacy of sequential disinfection processes, such as UF-UV-chlorination on intracellular (iARGs) and extracellular ARGs (eARGs), remains largely unknown. This study investigates the impact of this sequential disinfection process on the fate of iARGs, eARGs, and a crucial mobile genetic element (intI1) within a full-scale WWTP. Our findings revealed that the UF-UV-chlorination process effectively reduced the overall absolute abundance of detected ARGs in the effluent by 1.93 log, and intI1 by 0.86 log, compared to secondary effluent. The majority of these removals was achieved due to the UF and UV disinfection, while chlorination showed negligible impact on the absolute abundance of ARGs in the final effluent. Notably, five genera were identified as potential hosts for intI1 and eight iARGs, including aac(6')-Ib-cr, drfA1, sul1, sul2, ermB, mefA, tetA, and tetX, suggesting a high potential for horizontal gene transfer involving these ARGs. Overall, this study demonstrated that UF-UV-chlorination is a highly effective method for reducing ARGs in effluent from WWTPs.},
}

@article {pmid39752084,
year = {2025},
author = {Heiss, J and Huson, DH and Steel, M},
title = {Transformations to Simplify Phylogenetic Networks.},
journal = {Bulletin of mathematical biology},
volume = {87},
number = {2},
pages = {20},
pmid = {39752084},
issn = {1522-9602},
support = {23-UOC-003//Marsden Fund/ ; },
mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; Biological Evolution ; Evolution, Molecular ; },
abstract = {The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or lateral gene transfer events between lineages, and so the history of life is more accurately described by a rooted phylogenetic network. Nevertheless, phylogenetic networks may be complex and difficult to interpret, so biologists sometimes prefer a tree that summarises the central tree-like trend of evolution. In this paper, we formally investigate methods for transforming an arbitrary phylogenetic network into a tree (on the same set of leaves) and ask which ones (if any) satisfy a simple consistency condition. This consistency condition states that if we add additional species into a phylogenetic network (without otherwise changing this original network) then transforming this enlarged network into a rooted phylogenetic tree induces the same tree on the original set of species as transforming the original network. We show that the LSA (lowest stable ancestor) tree method satisfies this consistency property, whereas several other commonly used methods (and a new one we introduce) do not. We also briefly consider transformations that convert arbitrary phylogenetic networks to another simpler class, namely normal networks.},
}

*Phylogeny
*Mathematical Concepts
*Models, Genetic
Biological Evolution
Evolution, Molecular

@article {pmid39749146,
year = {2024},
author = {Chaves, CRS and Salamandane, A and Vieira, EJF and Salamandane, C},
title = {Antibiotic Resistance in Fermented Foods Chain: Evaluating the Risks of Emergence of Enterococci as an Emerging Pathogen in Raw Milk Cheese.},
journal = {International journal of microbiology},
volume = {2024},
number = {},
pages = {2409270},
pmid = {39749146},
issn = {1687-918X},
abstract = {Fermented foods, particularly fermented dairy products, offer significant health benefits but also present serious concerns. Probiotic bacteria, such as lactic acid bacteria (LAB), found in these foods have been strongly linked to the selection and dissemination of antibiotic resistance genes (ARGs). This study aims to examine the potential risks associated with fermented foods, despite their importance in human nutrition, by analyzing the entire production chain from raw material acquisition to storage. Focusing on cheese production as a key fermented food, the study will investigate various aspects, including dairy farm management, milk acquisition, milk handling, and the application of good manufacturing practices (GMP) and good hygiene practices (GHP) in cheese production. The findings of this review highlight that ARGs found in LAB are similar to those observed in hygiene indicator bacteria like E. coli and pathogens like S. aureus. The deliberate use of antibiotics in dairy farms and the incorrect use of disinfectants in cheese factories contribute to the prevalence of antibiotic-resistant bacteria in cheeses. Cheese factories, with their high frequency of horizontal gene transfer, are environments where the microbiological diversity of raw milk can enhance ARG transfer. The interaction between the raw milk microbiota and other environmental microbiotas, facilitated by cross-contamination, increases metabolic communication between bacteria, further promoting ARG transfer. Understanding these bacterial and ARG interactions is crucial to ensure food safety for consumers.},
}

@article {pmid39747694,
year = {2025},
author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA},
title = {Profiling lateral gene transfer events in the human microbiome using WAAFLE.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39747694},
issn = {2058-5276},
support = {K23DK125838//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; T32CA009001//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; U54DE023798//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
abstract = {Lateral gene transfer (LGT), also known as horizontal gene transfer, facilitates genomic diversification in microbial populations. While previous work has surveyed LGT in human-associated microbial isolate genomes, the landscape of LGT arising in personal microbiomes is not well understood, as there are no widely adopted methods to characterize LGT from complex communities. Here we developed, benchmarked and validated a computational algorithm (WAAFLE or Workflow to Annotate Assemblies and Find LGT Events) to profile LGT from assembled metagenomes. WAAFLE prioritizes specificity while maintaining high sensitivity for intergenus LGT. Applying WAAFLE to >2,000 human metagenomes from diverse body sites, we identified >100,000 high-confidence previously uncharacterized LGT (~2 per microbial genome-equivalent). These were enriched for mobile elements, as well as restriction-modification functions associated with the destruction of foreign DNA. LGT frequency was influenced by biogeography, phylogenetic similarity of involved pairs (for example, Fusobacterium periodonticum and F. nucleatum) and donor abundance. These forces manifest as networks in which hub taxa donate unequally with phylogenetic neighbours. Our findings suggest that human microbiome LGT may be more ubiquitous than previously described.},
}

@article {pmid39460620,
year = {2025},
author = {Zhu, Q and Chen, Q and Gao, S and Li, Z and Zhou, H and Cui, Z and Fan, G and Liu, X and Wu, X and Ma, J and Kan, B and Hu, S and Wu, L and Lu, X},
title = {PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D169-D178},
pmid = {39460620},
issn = {1362-4962},
support = {2021YFF0703805//National Key Research and Development Program of China/ ; XDB0830000//Chinese Academy of Sciences/ ; 2022YFC2602301//National Key Research and Development Program of China/ ; 22193064//National Natural Science Foundation of China/ ; SRPG22007//Self-supporting Program of Guangzhou National Laboratory/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Virulence Factors/genetics ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Humans ; Databases, Genetic ; Genome, Bacterial ; },
abstract = {Plasmids, as independent genetic elements, carrying resistance or virulence genes and transfer them among different pathogens, posing a significant threat to human health. Under the 'One Health' approach, it is crucial to control the spread of plasmids carrying such genes. To achieve this, a comprehensive characterization of plasmids in pathogens is essential. Here we present the Plasmids in Pathogens Database (PIPdb), a pioneering resource that includes 792 964 plasmid segment clusters (PSCs) derived from 1 009 571 assembled genomes across 450 pathogenic species from 110 genera. To our knowledge, PIPdb is the first database specifically dedicated to plasmids in pathogenic bacteria, offering detailed multi-dimensional metadata such as collection date, geographical origin, ecosystem, host taxonomy, and habitat. PIPdb also provides extensive functional annotations, including plasmid type, insertion sequences, integron, oriT, relaxase, T4CP, virulence factors genes, heavy metal resistance genes and antibiotic resistance genes. The database features a user-friendly interface that facilitates studies on plasmids across diverse host taxa, habitats, and ecosystems, with a focus on those carrying antimicrobial resistance genes (ARGs). We have integrated online tools for plasmid identification and annotation from assembled genomes. Additionally, PIPdb includes a risk-scoring system for identifying potentially high-risk plasmids. The PIPdb web interface is accessible at https://nmdc.cn/pipdb.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Virulence Factors/genetics
*Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Humans
Databases, Genetic
Genome, Bacterial

@article {pmid39373502,
year = {2025},
author = {Liu, G and Li, X and Guan, J and Tai, C and Weng, Y and Chen, X and Ou, HY},
title = {oriTDB: a database of the origin-of-transfer regions of bacterial mobile genetic elements.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D163-D168},
pmid = {39373502},
issn = {1362-4962},
support = {2023YFC2307103//National Key Research and Development Program of China/ ; 32070572//National Natural Science Foundation of China/ ; SHDC2022CRD039//Shanghai Hospital Development Center Foundation/ ; GWV1-11.2-XD01//Talent Program on Public Health System Construction of Shanghai/ ; 20240818//Shanghai Jiao Tong University School of Medicine/ ; },
mesh = {*Interspersed Repetitive Sequences ; Gene Transfer, Horizontal ; Plasmids/genetics ; Conjugation, Genetic ; Bacteria/genetics/classification ; Databases, Genetic ; Genome, Bacterial ; Bacterial Proteins/genetics/metabolism ; Databases, Nucleic Acid ; DNA, Bacterial/genetics ; },
abstract = {Conjugation and mobilization are two important pathways of horizontal transfer of bacterial mobile genetic elements (MGEs). The origin-of-transfer (oriT) region is crucial for this process, serving as a recognition site for relaxase and containing the DNA nicking site (nic site), which initiates the conjugation or mobilization. Here, we present a database of the origin-of-transfer regions of bacterial MGEs, oriTDB (https://bioinfo-mml.sjtu.edu.cn/oriTDB2/). Incorporating data from text mining and genome analysis, oriTDB comprises 122 experimentally validated and 22 927 predicted oriTs within bacterial plasmids, Integrative and Conjugative Elements, and Integrative and Mobilizable Elements. Additionally, oriTDB includes details about associated relaxases, auxiliary proteins, type IV coupling proteins, and a gene cluster encoding the type IV secretion system. The database also provides predicted secondary structures of oriT sequences, dissects oriT regions into pairs of inverted repeats, nic sites, and their flanking conserved sequences, and offers an interactive visual representation. Furthermore, oriTDB includes an enhanced oriT prediction pipeline, oriTfinder2, which integrates a functional annotation module for cargo genes in bacterial MGEs. This resource is intended to support research on bacterial conjugative or mobilizable elements and promote an understanding of their cargo gene functions.},
}

*Interspersed Repetitive Sequences
Gene Transfer, Horizontal
Plasmids/genetics
Conjugation, Genetic
Bacteria/genetics/classification
Databases, Genetic
Genome, Bacterial
Bacterial Proteins/genetics/metabolism
Databases, Nucleic Acid
DNA, Bacterial/genetics

@article {pmid39742307,
year = {2024},
author = {Lian, ZH and Salam, N and Tan, S and Yuan, Y and Li, MM and Li, YX and Liu, ZT and Hu, CJ and Lv, AP and OuYang, YT and Lu, CY and Zhang, JY and Chen, Y and Chen, LB and Luo, ZH and Ma, B and Hua, ZS and Jiao, JY and Li, WJ and Liu, L},
title = {Metagenomic analysis sheds light on the mixotrophic lifestyle of bacterial phylum Zhuqueibacterota.},
journal = {iMeta},
volume = {3},
number = {6},
pages = {e249},
pmid = {39742307},
issn = {2770-596X},
abstract = {Zhuqueibacterota is a novel bacterial phylum proposed based on hot spring metagenomes and public metagenome-assembled genomes, classified within the Fibrobacterota-Chlorobiota-Bacteroidota superphylum. This globally distributed phylum consists of one class and five orders, with the majority of its members being facultative anaerobes. Notably, the order Zhuqueibacterales utilizes hydrogen as an electron donor for carbon fixation through the Calvin Benson Bassham cycle. Phylogenetic and metabolic analyses reveal the phylum's key role in the carbon cycle, with frequent horizontal gene transfer events influencing its evolutionary trajectory.},
}

@article {pmid39740178,
year = {2024},
author = {Zahir, A and Okorie, PA and Nwobasi, VN and David, EI and Nwankwegu, RO and Azi, F},
title = {Harnessing Microbial Signal Transduction Systems in Natural and Synthetic Consortia for Biotechnological Applications.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.2707},
pmid = {39740178},
issn = {1470-8744},
abstract = {Signal transduction is crucial for communication and cellular response in microbial communities. Consortia rely on it for effective communication, responding to changing environmental conditions, establishing community structures, and performing collective behaviors. Microbial signal transduction can be through quorum sensing (QS), two-component signal transduction systems, biofilm formation, nutrient sensing, chemotaxis, horizontal gene transfer stress response, and so forth. The consortium uses small signaling molecules in QS to regulate gene expression and coordinate intercellular communication and behaviors. Biofilm formation allows cells to adhere and aggregate, promoting species interactions and environmental stress resistance. Chemotaxis enables directional movement toward or away from chemical gradients, promoting efficient resource utilization and community organization within the consortium. In recent years, synthetic microbial consortia have gained attention for their potential applications in biotechnology and bioremediation. Understanding signal transduction in natural and synthetic microbial consortia is important for gaining insights into community dynamics, evolution, and ecological function. It can provide strategies for biotechnological innovation for enhancing biosensors, biodegradation, bioenergy efficiency, and waste reduction. This review provides compelling insight that will advance our understanding of microbial signal transduction dynamics and its role in orchestrating microbial interactions, which facilitate coordination, cooperation, gene expression, resource allocation, and trigger specific responses that determine community success.},
}

@article {pmid39737801,
year = {2024},
author = {Singh, S and Selvakumar, S and Swaminathan, P},
title = {In silico targeting of AmpC beta-lactamases in Enterobacter cloacae: unveiling Piperenol B as a potent antimicrobial lead.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/07391102.2024.2446661},
pmid = {39737801},
issn = {1538-0254},
abstract = {Antimicrobial Resistance poses a major threat to human health worldwide. Microorganisms develop multi-drug resistance due to intrinsic factors, evolutionary chromosomal alterations, and horizontal gene transfer. Enterobacter cloacae, a common nosocomial bacterium, can cause various infections and is classified as multidrug-resistant. This species produces AmpC enzymes, serine beta-lactamases that hydrolyze beta-lactam antibiotics by cleaving their beta-lactam ring, contributing to its resistance. Traditionally, many phytoconstituents have been used for their antibacterial properties against microorganisms. This study explores phytocompounds to mitigate the effects of beta-lactamase enzymes. In this study, we selected 12592 phytoconstituents with antibacterial properties from Dr. Duke's Ethnobotanical and Phytochemical Database for the virtual screening process. Initial hits were selected based on highest docking scores and then filtered using the ADMET property. Among these, a promising compound Piperenol B showed the highest docking score of -9.1 kcal/mol. A 240 ns molecular dynamics simulation showed that Piperenol B maintained stable conformation and showed consistent results in multiple runs with AmpC protein. Piperenol B complex had a binding free energy score of -61.75 ± 8.0 kJ/mol, whereas the known AmpC inhibitor Clavulanic acid showed -46.64 ± 3.2 kJ/mol. Non-covalent contacts in protein-ligand interactions and specific subunit interfaces were examined using the Protein Contacts Atlas. The STRING database was used to construct the Protein-Protein interaction for AmpC and its interacting proteins. The findings of this study suggested that Piperenol B could be an effective inhibitor of the targeted AmpC protein in Enterobacter cloacae which requires validation in in vitro studies.},
}

@article {pmid39736215,
year = {2024},
author = {Wang, Y and Ge, J and Xian, W and Tang, Z and Xue, B and Yu, J and Yao, YF and Liu, H and Qiu, J and Liu, X},
title = {Phosphorylation of the prokaryotic histone-like protein H-NS modulates bacterial virulence in Salmonella Typhimurium.},
journal = {Microbiological research},
volume = {292},
number = {},
pages = {128041},
doi = {10.1016/j.micres.2024.128041},
pmid = {39736215},
issn = {1618-0623},
abstract = {H-NS is a prokaryotic histone-like protein that binds to bacterial chromosomal DNA with important regulatory roles in gene expression. Unlike histone proteins, hitherto post-translational modifications of H-NS are still largely uncharacterized, especially in bacterial pathogens. Salmonella Typhimurium is a primary enteric pathogen and its virulence is mainly dependent on specialized type III secretion systems (T3SSs), which were evolutionarily acquired via horizontal gene transfer. Previous studies have shown that H-NS plays a critical role in silencing foreign T3SS genes. Here, we found that H-NS is phosphorylated at multiple residues in S. Typhimurium, including S45, Y61, S78, S84, T86, and T106. Notably, we demonstrated that phosphorylation of H-NS S78 promotes its dissociation from DNA via a mechanism dependent on dimer formation, thereby leading to transcriptional activation of target genes. Functionally, phosphoryl-H-NS contributes to the expression of T3SS-associated proteins and hence increases bacterial virulence during infection. Therefore, our study reveals a novel mechanism by which covalent modifications of prokaryotic histone-like proteins regulate bacterial virulence of an important human pathogen.},
}

@article {pmid39733752,
year = {2024},
author = {Feng, B and Chen, J and Wang, C and Wang, P and You, G and Lin, J and Gao, H},
title = {Removal of ofloxacin and inhibition of antibiotic resistance gene spread during the aerobic biofilm treatment of rural domestic sewage through the micro-nano aeration technology.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {137020},
doi = {10.1016/j.jhazmat.2024.137020},
pmid = {39733752},
issn = {1873-3336},
abstract = {Micro-nano aeration (MNA) has great potential for emerging contaminant removal. However, the mechanism of antibiotic removal and antibiotic resistance gene (ARG) spread, and the impact of the different aeration conditions remain unclear. This study investigated the adsorption and biodegradation of ofloxacin (OFL) and the spread of ARGs in aerobic biofilm systems under MNA and conventional aeration (CVA) conditions. Results showed that the MNA increased OFL removal by 17.27 %-40.54 % and decreased total ARG abundance by 36.37 %-54.98 %, compared with CVA. MNA-induced biofilm rough morphology, high zeta potential, and reduced extracellular polymeric substance (EPS) secretion enhanced OFL adsorption. High dissolved oxygen and temperature, induced by MNA-enriched aerobic bacteria and their carrying OFL-degrading genes, enhanced OFL biodegradation. MNA inhibited the enrichment of ARG host bacteria, which acquired ARGs possibly via horizontal gene transfer (HGT). Functional profiles involved in the HGT process, including reactive oxygen species production, membrane permeability, mobile genetic elements (MGEs), adenosine triphosphate synthesis, and EPS secretion, were down-regulated by MNA, inhibiting ARG spread. Partial least-squares path modeling revealed that MGEs might be the main factor inhibiting ARG spread. This study provides insights into the mechanisms by which MNA enhances antibiotic removal and inhibits ARG spread in aerobic biofilm systems.},
}